<?xml version='1.0'?><rss version="2.0" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:georss="http://www.georss.org/georss" xmlns:atom="http://www.w3.org/2005/Atom" >
<channel>
	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/3868?offset=430</link>
	<atom:link href="https://bioinformaticsonline.com/related/3868?offset=430" rel="self" type="application/rss+xml" />
	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44561/bactopia-a-flexible-pipeline-for-complete-analysis-of-bacterial-genomes</guid>
	<pubDate>Sat, 08 Jun 2024 16:25:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44561/bactopia-a-flexible-pipeline-for-complete-analysis-of-bacterial-genomes</link>
	<title><![CDATA[Bactopia: a flexible pipeline for complete analysis of bacterial genomes]]></title>
	<description><![CDATA[<p>Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!</p>
<p>Bactopia was inspired by&nbsp;<a href="https://staphopia.github.io/">Staphopia</a>, a workflow we (Tim Read and myself) released that is targeted towards&nbsp;<em>Staphylococcus aureus</em>&nbsp;genomes. Using what we learned from Staphopia and user feedback, Bactopia was developed from scratch with usability, portability, and speed in mind from the start.</p>
<p>Bactopia uses&nbsp;<a href="https://www.nextflow.io/">Nextflow</a>&nbsp;to manage the workflow, allowing for support of many types of environments (e.g. cluster or cloud). Bactopia allows for the usage of many public datasets as well as your own datasets to further enhance the analysis of your sequencing. Bactopia only uses software packages available from&nbsp;<a href="https://bioconda.github.io/">Bioconda</a>&nbsp;and&nbsp;<a href="https://conda-forge.org/">Conda-Forge</a>&nbsp;to make installation as simple as possible for&nbsp;<em>all</em>&nbsp;users.</p>
<p>To highlight the use of&nbsp;<a href="https://bactopia.github.io/latest/full-guide/">Bactopia</a>&nbsp;and&nbsp;<a href="https://bactopia.github.io/latest/bactopia-tools/">Bactopia Tools</a>, we performed an analysis of 1,664 public&nbsp;<em>Lactobacillus</em>&nbsp;genomes, focusing on&nbsp;<em>Lactobacillus crispatus</em>, a species that is a common part of the human vaginal microbiome. The results from this analysis are published in mSystems under the title:&nbsp;<em><a href="https://doi.org/10.1128/mSystems.00190-20">Bactopia: a flexible pipeline for complete analysis of bacterial genomes</a></em></p>
<p><a href="https://bactopia.github.io/latest/assets/bactopia-workflow.png"><img src="https://bactopia.github.io/latest/assets/bactopia-workflow.png" alt="Bactopia Workflow" style="border: 0px;"></a></p><p>Address of the bookmark: <a href="https://bactopia.github.io/latest/" rel="nofollow">https://bactopia.github.io/latest/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/923/phylogenetic-for-bioinformatics</guid>
	<pubDate>Tue, 16 Jul 2013 03:50:30 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/923/phylogenetic-for-bioinformatics</link>
	<title><![CDATA[Phylogenetic for Bioinformatics]]></title>
	<description><![CDATA[<p>Biologists estimate that there are about 5 to 100 million species of organisms living on Earth today. Evidence from morphological, biochemical, and gene sequence data suggests that all organisms on Earth are genetically related, and the genealogical relationships of living things can be represented by a vast evolutionary tree, the Tree of Life. The Tree of Life then represents the phylogeny of organisms, i. e., the history of organismal lineages as they change through time.<br />Every living organism contains DNA, RNA, and proteins. Closely related organisms generally have a high degree of agreement in the molecular structure of these substances, while the molecules of organisms distantly related usually show a pattern of dissimilarity. Molecular phylogeny uses such data to build a "relationship tree" that shows the probable evolution of various organisms. Not until recent decades, however, has it been possible to isolate and identify these molecular structures.&nbsp;<br />phylogenetics is the study of evolutionary relatedness among various groups of organisms (for example, species or populations), which is discovered through molecular sequencing data and morphological data matrices. In other word, Phylogenetics, the science of phylogeny, is one part of the larger field of systematics, which also includes taxonomy. Taxonomy is the science of naming and classifying the diversity of organisms Molecular phylogeny is the use of the structure of molecules to gain information on an organism's evolutionary relationships. The result of a molecular phylogenetic analysis is expressed in a so-called phylogenetic tree.</p><p>The evolutionary connections between organisms are represented graphically through phylogenetic trees. Due to the fact that evolution takes place over long periods of time that cannot be observed directly, biologists must reconstruct phylogenies by inferring the evolutionary relationships among present-day organisms.&nbsp;<br />Application of the techniques that make this possible can be seen in the very limited field of human genetics, such as the ever more popular use of genetic testing to determine a child's paternity, as well as the emergence of a new branch of criminal forensics focused on genetic evidence.<br />The effect on traditional scientific classification schemes in the biological sciences has been dramatic as well. Work that was once immensely labor- and materials-intensive can now be done quickly and easily, leading to yet another source of information becoming available for systematic and taxonomic appraisal. This particular kind of data has become so popular that taxonomical schemes based solely on molecular data may be encountered. Proponents even claim that taxonomy was previously based on morphology alone, which of course is utter fable.<br /><br /><strong>For additional information on phylogenetics, see list of Phylogenetics Resources on the Internet.</strong></p><p>Phylogeny and Reconstructing Phylogenetic Trees:&nbsp;<a href="http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html"></a><a href="http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html">http://aleph0.clarku.edu/~djoyce/java/Phyltree/cover.html</a><br />the CBRG and Department of Statistics Phylogeny tutorial:&nbsp;<a href="http://www.compbio.ox.ac.uk/tutorials/phylogeny/"></a><a href="http://www.compbio.ox.ac.uk/tutorials/phylogeny/">http://www.compbio.ox.ac.uk/tutorials/phylogeny/</a><br />TUTORIAL: PHYLOGENETIC ANALYSIS USING PARSIMONY:<a href="http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html"></a><a href="http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html">http://home.cc.umanitoba.ca/~psgendb/GDE/phylogeny/parsimony/phylip.parsimony.html</a></p><p>PHYLIP:&nbsp;<a href="http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html"></a><a href="http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html">http://www.umanitoba.ca/afs/plant_science/psgendb/doc/Phylip/main.html</a><br />An Introduction to Molecular Phylogeny:&nbsp;<a href="http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf"></a><a href="http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf">http://bibiserv.techfak.uni-bielefeld.de/gcb04/tutorials/hoef-emden/GCB04Tut.pdf</a></p><p>How to make a phylogenetic tree:&nbsp;<a href="http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Tree"></a><a href="http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Tree">http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Tree</a>tutorial.html<br />Phylogenetic Trees:&nbsp;<a href="http://cnx.org/content/m11052/latest/"></a><a href="http://cnx.org/content/m11052/latest/">http://cnx.org/content/m11052/latest/</a><br />Phylogeny by Ron Shamir:&nbsp;<a href="http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf"></a><a href="http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf">http://www.cs.tau.ac.il/~rshamir/algmb/01/scribe08/lec08.pdf</a><br />Introduction to Phylogeny:&nbsp;<a href="http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm"></a><a href="http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm">http://www.utm.edu/departments/cens/biology/rirwin/391/391Phylog.htm</a><br />Lecturer notes on Phylogeny:&nbsp;<a href="http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf"></a><a href="http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf">http://www.sbc.su.se/~bens/course_material/phylocourse1/lecture2.pdf</a><br />Principles and Practice of Phylogenetic Systematics:<a href="http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm"></a><a href="http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm">http://www.faculty.biol.ttu.edu/Strauss/Phylogenetics/LectureNotes.htm</a></p><p>Inferring phylogenetic trees:&nbsp;<a href="http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf"></a><a href="http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf">http://www.cis.hut.fi/Opinnot/T-61.6070/slides2008/pres_6070.pdf</a></p><p><strong>Lecture Notes</strong></p><p>Chapter 1 - The Diversity, Classification, and Evolution of Vertebrates:<a href="http://academic.emporia.edu/mooredwi/nathist/chap1.htm"></a><a href="http://academic.emporia.edu/mooredwi/nathist/chap1.htm">http://academic.emporia.edu/mooredwi/nathist/chap1.htm</a></p><p>Algorithms for Phylogenetic Reconstructions:<a href="http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf"></a><a href="http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf">http://lectures.molgen.mpg.de/Algorithmische_Bioinformatik_WS0405/phylogeny_script.pdf</a></p><p>Phylogeny.fr is a free, simple to use web service dedicated to reconstructing and analysing phylogenetic relationships between molecular sequences. Phylogeny.fr runs and connects various bioinformatics programs to reconstruct a robust phylogenetic tree from a set of sequences. For more detail :&nbsp;<a href="http://www.phylogeny.fr/version2_cgi/index.cgi"></a><a href="http://www.phylogeny.fr/version2_cgi/index.cgi">http://www.phylogeny.fr/version2_cgi/index.cgi</a></p><p>A Brief Tutorial on Phylogenetics<br /><a href="http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf"></a><a href="http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf">http://bioss.ac.uk/~dirk/talks/tutorial_phylogenetics.pdf</a></p><p>A Brief Tutorial on Phylogenetics Human Rabbit Chicken<br /><a href="http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf"></a><a href="http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf">http://bioss.ac.uk/~dirk/talks/psnup_tutorial_phylogenetics.pdf</a></p><p>Phylogenetic Tree Computation Tutorial Overview<br /><a href="http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf"></a><a href="http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf">http://pga.lbl.gov/Workshop/April2002/lectures/Olken.pdf</a></p><p>MrBayes: A program for the Bayesian inference of phylogeny<br /><a href="http://golab.unl.edu/teaching/SBseminar/manual.pdf"></a><a href="http://golab.unl.edu/teaching/SBseminar/manual.pdf">http://golab.unl.edu/teaching/SBseminar/manual.pdf</a></p><p><strong>Web sites providing software for the construction of phylogenetic trees</strong></p><ul>
<li><a href="http://www.mbio.ncsu.edu/BioEdit/bioedit.html">BioEdit</a></li>
</ul><ul>
<li><a href="http://www.dinofish.com/">Coelocanth-Fish Out of Time</a></li>
</ul><ul>
<li><a href="http://cbrg.inf.ethz.ch/">Computational Biochemistry Research Group</a></li>
</ul><ul>
<li><a href="http://www.geocities.com/RainForest/Vines/8695/software.html">Digital Taxonomy</a></li>
</ul><ul>
<li><a href="http://www.cladistics.org/education/hennig86.html">Hennig 86</a></li>
</ul><ul>
<li><a href="http://www.bioinformaticssolutions.com/">Hyperclean</a>&nbsp;from Bioinformatics Solutions, Inc.</li>
</ul><ul>
<li><a href="http://www.mun.ca/biology/scarr/Directory.html">Memorial University of Newfoundland</a></li>
</ul><ul>
<li><a href="http://morphbank.ebc.uu.se/mrbayes/">Mr. Bayes</a></li>
</ul><ul>
<li><a href="http://www.cladistics.com/about_nona.htm">NONA</a></li>
</ul><ul>
<li><a href="http://evolve.zoo.ox.ac.uk/">Oxford University Evolutionary Biology Group</a></li>
</ul><ul>
<li><a href="http://flatpebble.nceas.ucsb.edu/public/">Paleobiology Database</a></li>
</ul><ul>
<li><a href="http://paup.csit.fsu.edu/index.html">PAUP</a></li>
</ul><ul>
<li><a href="http://evolution.genetics.washington.edu/phylip.html">Phylip Homepage</a></li>
</ul><ul>
<li><a href="http://research.amnh.org/scicomp/projects/poy.php">Poy</a></li>
</ul><ul>
<li><a href="http://www.sinauer.com/">Sinauer Associates</a></li>
</ul><ul>
<li><a href="http://www.cladistics.org/downloads/webtnt.html">TNT</a>-Tree Analysis Using New Technology</li>
</ul><ul>
<li><a href="http://www.treebase.org/treebase/index.html">Tree Base</a></li>
</ul><ul>
<li><a href="http://www.treefinder.de/">Treefinder</a></li>
</ul><ul>
<li><a href="http://www.tree-puzzle.de/">Tree-Puzzle</a></li>
</ul><ul>
<li><a href="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html">Tree View</a>-Taxonomy and Systematics Group at Glasgow</li>
</ul><ul>
<li><a href="http://evolution.genetics.washington.edu/phylip/software.html">Washington University</a>-List of Phylogeny Software</li>
</ul>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/3013/python-and-biopython-tutorial</guid>
	<pubDate>Fri, 23 Aug 2013 06:47:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/3013/python-and-biopython-tutorial</link>
	<title><![CDATA[Python and BioPython Tutorial]]></title>
	<description><![CDATA[<p>A quickstart tutorial that allows to become familiar with the Python language. The exercises expect knowledge of basic concepts of programming. A group of 2nd year computer science students with no previous Python knowledge required 60'-90' to complete the exercises. With about 3 hours time, the exercise is suitable for non-programmers as well.</p><p>Address of the bookmark: <a href="http://www.biotnet.org/training-materials/python-programmers" rel="nofollow">http://www.biotnet.org/training-materials/python-programmers</a></p>]]></description>
	<dc:creator>Manshi Raghubanshi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/10394/bioinformatics-protocols</guid>
	<pubDate>Mon, 05 May 2014 10:21:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/10394/bioinformatics-protocols</link>
	<title><![CDATA[Bioinformatics Protocols]]></title>
	<description><![CDATA[<h2><span> RNA Seq </span></h2>
<p><strong> Basic Galaxy Tutorial </strong></p>
<ul>
<li><a href="https://docs.google.com/document/pub?id=1KbTiBHtvHLfPRZ39AY3uriazrINA8TJzgjjwn1zPP7Y">RNA-Seq tutorial</a> based on <a href="http://www.nature.com/protocolexchange/protocols/2327">Trapnell et al. (2012)</a> <em>Nature Protocols</em></li>
</ul>
<dl><dd>In this tutorial we cover the concepts of <a href="http://en.wikipedia.org/wiki/RNA-Seq">RNA-Seq</a> differential gene expression (DGE) analysis using a very small synthetic dataset from a well studied organism.</dd></dl>
<p><strong> Advanced Galaxy Tutorial </strong></p>
<ul>
<li><a href="https://docs.google.com/document/d/1fQ1XfeOKhezJUDTzMXtZVY20c3RGoHe-HLvFOGzqU4s/pub">RNA-Seq (Advanced) Tutorial</a></li>
</ul>
<dl><dd>In this tutorial we compare the performance of three statistically-based differential expression tools:</dd><dd>* CuffDiff</dd><dd>* EdgeR</dd><dd>* DESeq2</dd></dl>
<p><strong> Advanced Command Line Tutorial </strong></p>
<ul>
<li><a href="https://docs.google.com/document/d/1ayJXtgBP1OXtnV7o7lq4QHKMNk5SdPHFq4hGkqndBtI/pub">Graphical Output with CummeRbund</a> introduces some basic commands using the cummeRbund package of the R programming language</li>
</ul>
<dl><dd>You will need to install R, RStudio and cummeRbund on your PC (explained in the Tutorial). You will learn how to produce graphical output from RNA-Seq analysis previously done using a Cuffdiff analysis.</dd></dl>
<h2><span> Variant Detection </span></h2>
<p><strong> Basic Galaxy Tutorial </strong></p>
<ul>
<li><a href="https://docs.google.com/document/pub?id=1ZRzrjjOCvtAu3m-IKL-rbJ1f4On60dDL_IEwG7oejdI">Variant Detection tutorial</a></li>
</ul>
<dl><dd>In this tutorial we cover the concepts of detecting small variants (SNVs and indels) in human genomic DNA using a small set of reads from chromosome 22.</dd></dl>
<p><strong>Advanced Galaxy Tutorial</strong></p>
<ul>
<li><a href="https://docs.google.com/document/pub?id=1CuKkKylVDb03tnN7RSWl5EUzleetn0ctjmvaidPKLxM">Variant Detection (Advanced) Tutorial</a></li>
</ul>
<dl><dd>In this tutorial we compare the performance of three statistically-based variant detection tools:</dd><dd>* SAMtools: Mpileup</dd><dd>* GATK: Unified Genotyper</dd><dd>* FreeBayes</dd><dd>Each of these tools takes as its input a BAM file of aligned reads and generates a list of likely variants in VCF format</dd></dl>
<p><strong>Pipelines</strong> are for those who are comfortable with using the UNIX command line; and often allow more control over branching and iteration logic.</p>
<ul>
<li><a href="https://github.com/claresloggett/variant_calling_pipeline">WGS/exome GATK-based variant calling pipeline</a></li>
</ul>
<dl><dd>This is a basic variant-calling and annotation pipeline developed at the Victorian Life Sciences Computation Initiative (VLSCI), University of Melbourne. It is based around BWA, GATK and ENSEMBL and was originally designed for human (or similar) data. The master branch is configured for WGS data; there is an exome branch configured for variant calling in exome data.</dd><dd>To run the pipeline you will need Rubra: <a href="https://github.com/bjpop/rubra">https://github.com/bjpop/rubra</a>. Rubra uses the python Ruffus library: <a href="http://www.ruffus.org.uk/">http://www.ruffus.org.uk/</a>.</dd></dl>
<p><strong>Protocols</strong></p>
<ul>
<li><a href="https://docs.google.com/document/d/1lfDYNzHjfDA1pHTHd-0w3xHhg7L4TipT1gRfzgiV8es/pub">Familial Variant Calling</a></li>
</ul>
<dl><dd>In this protocol we discuss and outline the process of calling familial related mutations.</dd></dl>
<ul>
<li><a href="https://docs.google.com/document/d/1PIhm8NrFGaSK0hxpDcp8wUOz11ZkOaHIrpnJshMgDec/pub">Somatic Variant Calling</a></li>
</ul>
<dl><dd>In this protocol we discuss and outline the process of identifying somatic variants or mutations.</dd></dl>
<h2><span> Assembly </span></h2>
<p><strong> Basic Galaxy Tutorial </strong></p>
<ul>
<li><a href="https://docs.google.com/document/pub?id=1N3AB9ptISUu4zULqe1kXpVF0BDyGb5f5yzxWSJd_WNM">Genome assembly tutorial</a></li>
</ul>
<dl><dd>In this tutorial we carry out de novo assembly of a microbial genome. We have also written a <a href="https://docs.google.com/document/d/1xs-TI5MejQARqo0pcocGlymsXldwJbJII890gnmjI0o/pub">De novo Genome Assembly for Illumina Data</a> Protocol for a more generic description of the method.</dd></dl>
<p><strong> Protocol </strong></p>
<ul>
<li><a href="https://docs.google.com/document/d/1xs-TI5MejQARqo0pcocGlymsXldwJbJII890gnmjI0o/pub">De novo Genome Assembly for Illumina Data</a></li>
</ul>
<dl><dd>In this protocol we discuss and outline the process of de novo assembly for small to medium sized genomes. Use our <a href="https://docs.google.com/document/pub?id=1N3AB9ptISUu4zULqe1kXpVF0BDyGb5f5yzxWSJd_WNM">Genome assembly tutorial</a> to learn a specific case of using Galaxy to carry out de novo assembly of a microbial genome.</dd></dl>
<h2><span> Small RNAs </span></h2>
<p><strong> Basic Galaxy Tutorial </strong></p>
<ul>
<li><a href="https://docs.google.com/document/d/1WAObJr7M0m8U-2ku-0Y0Sdt_IHmqd1h8WaJHPhnJ1lM/pub">Quality control for small RNA</a></li>
</ul>
<dl><dd>This tutorial covers initial steps of the workflow for analysis of short RNA expression such as a quality control of the raw reads, processing of the raw reads for the subsequent analysis and initial quality assessment of the library.</dd></dl>
<h2><span> ChIP Seq </span></h2>
<p><strong> Protocol </strong></p>
<ul>
<li><a href="https://docs.google.com/document/d/1UPJC8dsiDeP5R9MH9U0IvoDgPF2Q3EOstAuzS3e6WCE/pub">ChIP-Seq</a></li>
</ul>
<dl><dd>In this protocol we discuss ChIP-Seq: a method to analyze the interaction between proteins and DNA.</dd></dl>
<h2><span> Amplicons </span></h2>
<p><strong>Protocol</strong></p>
<ul>
<li><a href="https://docs.google.com/document/d/1uW7JzxG86QzS92hTyeuNsLhX_d1XFbaZPSjh7jWxcSg/pub">Amplicon Alignment</a></li>
</ul>
<dl><dd>In this protocol we discuss and outline the process of aligning custom amplicons using primers for high precision.</dd></dl>
<h2><span> Learn Galaxy </span></h2>
<p><a href="https://docs.google.com/document/d/1wsdJDYfjZVg2uJxm9AHi_j0mY3X1M1F4gB-elkuYL7c/pub">Introduction to Galaxy,</a> for those who are very new to Galaxy.</p>
<p><a href="https://docs.google.com/document/d/1t7vVqa3mdeZYPv5-8hiHBFBYhNiynV_3mWByno9-wUM/pub">Using Histories and Workflows,</a> for those with some Galaxy knowledge.</p>
<p>The Galaxy project website has many <a href="http://wiki.galaxyproject.org/Learn">tutorials</a> and <a href="http://wiki.galaxyproject.org/Learn/Screencasts">screencasts</a> about using Galaxy and the tools, and developing new tools.</p><p>Address of the bookmark: <a href="https://genome.edu.au/wiki/Learn" rel="nofollow">https://genome.edu.au/wiki/Learn</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/23516/visual-machine-learning</guid>
	<pubDate>Wed, 29 Jul 2015 04:29:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/23516/visual-machine-learning</link>
	<title><![CDATA[Visual machine learning !!!]]></title>
	<description><![CDATA[<p>In machine learning, computers apply <strong>statistical learning</strong> techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions.</p>
<p>More at http://www.r2d3.us/visual-intro-to-machine-learning-part-1/</p><p>Address of the bookmark: <a href="http://www.r2d3.us/visual-intro-to-machine-learning-part-1/" rel="nofollow">http://www.r2d3.us/visual-intro-to-machine-learning-part-1/</a></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/26426/genome-browser-gbrowse</guid>
	<pubDate>Fri, 19 Feb 2016 09:22:43 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26426/genome-browser-gbrowse</link>
	<title><![CDATA[Genome Browser : GBrowse]]></title>
	<description><![CDATA[<p>Generic Genome Browser Version 2: A Tutorial for Administrators</p>
<p>This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD, BioPerl and the other GBrowse dependencies. If you haven't, please see the <a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO">GBrowse HOWTO</a> During most of the tutorial, we will be using the "in-memory" GBrowse database (no relational database required!) Later we will show how to set up a genome size database using the berkeleydb and MySQL adaptors.</p>
<p>More at http://elp.ucdavis.edu/tutorial/tutorial.html</p><p>Address of the bookmark: <a href="http://elp.ucdavis.edu/tutorial/tutorial.html" rel="nofollow">http://elp.ucdavis.edu/tutorial/tutorial.html</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44200/dashboard-designing-tutorial</guid>
	<pubDate>Thu, 02 Mar 2023 06:48:43 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44200/dashboard-designing-tutorial</link>
	<title><![CDATA[Dashboard designing tutorial !]]></title>
	<description><![CDATA[<p>Dashboard Design Tutorial</p><p>Address of the bookmark: <a href="https://github.com/dthill196/SARS-2-Dashboard-Tutorial" rel="nofollow">https://github.com/dthill196/SARS-2-Dashboard-Tutorial</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34413/coursera-genome-assembly-tutorial</guid>
	<pubDate>Sat, 25 Nov 2017 08:57:25 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34413/coursera-genome-assembly-tutorial</link>
	<title><![CDATA[coursera genome assembly tutorial]]></title>
	<description><![CDATA[<p><span>Solutions to Coursera Genome Sequencing (Bioinformatics II)</span></p><p>Address of the bookmark: <a href="https://github.com/iansealy/coursera-assembly" rel="nofollow">https://github.com/iansealy/coursera-assembly</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</guid>
	<pubDate>Fri, 26 Apr 2019 16:19:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</link>
	<title><![CDATA[AWK for beginners !]]></title>
	<description><![CDATA[<p>AWK is a standard tool on every POSIX-compliant UNIX system. It&rsquo;s like flex/lex, from the command-line, perfect for text-processing tasks and other scripting needs. It has a C-like syntax, but without mandatory semicolons (although, you should use them anyway, because they are required when you&rsquo;re writing one-liners, something AWK excels at), manual memory management, or static typing. It excels at text processing. You can call to it from a shell script, or you can use it as a stand-alone scripting language.</p><p>Why use AWK instead of Perl? Readability. AWK is easier to read than Perl. For simple text-processing scripts, particularly ones that read files line by line and split on delimiters, AWK is probably the right tool for the job.</p><div><pre><span>#!/usr/bin/awk -f</span>

<span># Comments are like this</span>


<span># AWK programs consist of a collection of patterns and actions.</span>
<span>pattern1</span> <span>{</span> <span>action</span><span>;</span> <span>}</span> <span># just like lex</span>
<span>pattern2</span> <span>{</span> <span>action</span><span>;</span> <span>}</span>

<span># There is an implied loop and AWK automatically reads and parses each</span>
<span># record of each file supplied. Each record is split by the FS delimiter,</span>
<span># which defaults to white-space (multiple spaces,tabs count as one)</span>
<span># You can assign FS either on the command line (-F C) or in your BEGIN</span>
<span># pattern</span>

<span># One of the special patterns is BEGIN. The BEGIN pattern is true</span>
<span># BEFORE any of the files are read. The END pattern is true after</span>
<span># an End-of-file from the last file (or standard-in if no files specified)</span>
<span># There is also an output field separator (OFS) that you can assign, which</span>
<span># defaults to a single space</span>

<span>BEGIN</span> <span>{</span>

    <span># BEGIN will run at the beginning of the program. It's where you put all</span>
    <span># the preliminary set-up code, before you process any text files. If you</span>
    <span># have no text files, then think of BEGIN as the main entry point.</span>

    <span># Variables are global. Just set them or use them, no need to declare..</span>
    <span>count</span> <span>=</span> <span>0</span><span>;</span>

    <span># Operators just like in C and friends</span>
    <span>a</span> <span>=</span> <span>count</span> <span>+</span> <span>1</span><span>;</span>
    <span>b</span> <span>=</span> <span>count</span> <span>-</span> <span>1</span><span>;</span>
    <span>c</span> <span>=</span> <span>count</span> <span>*</span> <span>1</span><span>;</span>
    <span>d</span> <span>=</span> <span>count</span> <span>/</span> <span>1</span><span>;</span> <span># integer division</span>
    <span>e</span> <span>=</span> <span>count</span> <span>%</span> <span>1</span><span>;</span> <span># modulus</span>
    <span>f</span> <span>=</span> <span>count</span> <span>^</span> <span>1</span><span>;</span> <span># exponentiation</span>

    <span>a</span> <span>+=</span> <span>1</span><span>;</span>
    <span>b</span> <span>-=</span> <span>1</span><span>;</span>
    <span>c</span> <span>*=</span> <span>1</span><span>;</span>
    <span>d</span> <span>/=</span> <span>1</span><span>;</span>
    <span>e</span> <span>%=</span> <span>1</span><span>;</span>
    <span>f</span> <span>^=</span> <span>1</span><span>;</span>

    <span># Incrementing and decrementing by one</span>
    <span>a</span><span>++</span><span>;</span>
    <span>b</span><span>--</span><span>;</span>

    <span># As a prefix operator, it returns the incremented value</span>
    <span>++</span><span>a</span><span>;</span>
    <span>--</span><span>b</span><span>;</span>

    <span># Notice, also, no punctuation such as semicolons to terminate statements</span>

    <span># Control statements</span>
    <span>if</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span>
        <span>print</span> <span>"Starting with count of 0"</span><span>;</span>
    <span>else</span>
        <span>print</span> <span>"Huh?"</span><span>;</span>

    <span># Or you could use the ternary operator</span>
    <span>print</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span> <span>?</span> <span>"Starting with count of 0"</span> <span>:</span> <span>"Huh?"</span><span>;</span>

    <span># Blocks consisting of multiple lines use braces</span>
    <span>while</span> <span>(</span><span>a</span> <span>&lt;</span> <span>10</span><span>)</span> <span>{</span>
        <span>print</span> <span>"String concatenation is done"</span> <span>" with a series"</span> <span>" of"</span>
            <span>" space-separated strings"</span><span>;</span>
        <span>print</span> <span>a</span><span>;</span>

        <span>a</span><span>++</span><span>;</span>
    <span>}</span>

    <span>for</span> <span>(</span><span>i</span> <span>=</span> <span>0</span><span>;</span> <span>i</span> <span>&lt;</span> <span>10</span><span>;</span> <span>i</span><span>++</span><span>)</span>
        <span>print</span> <span>"Good ol' for loop"</span><span>;</span>

    <span># As for comparisons, they're the standards:</span>
    <span># a &lt; b   # Less than</span>
    <span># a &lt;= b  # Less than or equal</span>
    <span># a != b  # Not equal</span>
    <span># a == b  # Equal</span>
    <span># a &gt; b   # Greater than</span>
    <span># a &gt;= b  # Greater than or equal</span>

    <span># Logical operators as well</span>
    <span># a &amp;&amp; b  # AND</span>
    <span># a || b  # OR</span>

    <span># In addition, there's the super useful regular expression match</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>
    <span>if</span> <span>(</span><span>"boo"</span> <span>!~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Boo!"</span><span>;</span>

    <span># Arrays</span>
    <span>arr</span><span>[</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>arr</span><span>[</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>

    <span># You can also initialize an array with the built-in function split()</span>

    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo:bar:baz"</span><span>,</span> <span>arr</span><span>,</span> <span>":"</span><span>);</span>

    <span># You also have associative arrays (actually, they're all associative arrays)</span>
    <span>assoc</span><span>[</span><span>"foo"</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>assoc</span><span>[</span><span>"bar"</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>

    <span># And multi-dimensional arrays, with some limitations I won't mention here</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"boo"</span><span>;</span>

    <span># You can test for array membership</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>

    <span># You can also use the 'in' operator to traverse the keys of an array</span>
    <span>for</span> <span>(</span><span>key</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>assoc</span><span>[</span><span>key</span><span>];</span>

    <span># The command line is in a special array called ARGV</span>
    <span>for</span> <span>(</span><span>argnum</span> <span>in</span> <span>ARGV</span><span>)</span>
        <span>print</span> <span>ARGV</span><span>[</span><span>argnum</span><span>];</span>

    <span># You can remove elements of an array</span>
    <span># This is particularly useful to prevent AWK from assuming the arguments</span>
    <span># are files for it to process</span>
    <span>delete</span> <span>ARGV</span><span>[</span><span>1</span><span>];</span>

    <span># The number of command line arguments is in a variable called ARGC</span>
    <span>print</span> <span>ARGC</span><span>;</span>

    <span># AWK has several built-in functions. They fall into three categories. I'll</span>
    <span># demonstrate each of them in their own functions, defined later.</span>

    <span>return_value</span> <span>=</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>);</span>
    <span>string_functions</span><span>();</span>
    <span>io_functions</span><span>();</span>
<span>}</span>

<span># Here's how you define a function</span>
<span>function</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>,</span>     <span>d</span><span>)</span> <span>{</span>

    <span># Probably the most annoying part of AWK is that there are no local</span>
    <span># variables. Everything is global. For short scripts, this is fine, even</span>
    <span># useful, but for longer scripts, this can be a problem.</span>

    <span># There is a work-around (ahem, hack). Function arguments are local to the</span>
    <span># function, and AWK allows you to define more function arguments than it</span>
    <span># needs. So just stick local variable in the function declaration, like I</span>
    <span># did above. As a convention, stick in some extra whitespace to distinguish</span>
    <span># between actual function parameters and local variables. In this example,</span>
    <span># a, b, and c are actual parameters, while d is merely a local variable.</span>

    <span># Now, to demonstrate the arithmetic functions</span>

    <span># Most AWK implementations have some standard trig functions</span>
    <span>localvar</span> <span>=</span> <span>sin</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>cos</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>atan2</span><span>(</span><span>b</span><span>,</span> <span>a</span><span>);</span> <span># arc tangent of b / a</span>

    <span># And logarithmic stuff</span>
    <span>localvar</span> <span>=</span> <span>exp</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>log</span><span>(</span><span>a</span><span>);</span>

    <span># Square root</span>
    <span>localvar</span> <span>=</span> <span>sqrt</span><span>(</span><span>a</span><span>);</span>

    <span># Truncate floating point to integer</span>
    <span>localvar</span> <span>=</span> <span>int</span><span>(</span><span>5.34</span><span>);</span> <span># localvar =&gt; 5</span>

    <span># Random numbers</span>
    <span>srand</span><span>();</span> <span># Supply a seed as an argument. By default, it uses the time of day</span>
    <span>localvar</span> <span>=</span> <span>rand</span><span>();</span> <span># Random number between 0 and 1.</span>

    <span># Here's how to return a value</span>
    <span>return</span> <span>localvar</span><span>;</span>
<span>}</span>

<span>function</span> <span>string_functions</span><span>(</span>    <span>localvar</span><span>,</span> <span>arr</span><span>)</span> <span>{</span>

    <span># AWK, being a string-processing language, has several string-related</span>
    <span># functions, many of which rely heavily on regular expressions.</span>

    <span># Search and replace, first instance (sub) or all instances (gsub)</span>
    <span># Both return number of matches replaced</span>
    <span>localvar</span> <span>=</span> <span>"fooooobar"</span><span>;</span>
    <span>sub</span><span>(</span><span>"fo+"</span><span>,</span> <span>"Meet me at the "</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "Meet me at the bar"</span>
    <span>gsub</span><span>(</span><span>"e+"</span><span>,</span> <span>"."</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "m..t m. at th. bar"</span>

    <span># Search for a string that matches a regular expression</span>
    <span># index() does the same thing, but doesn't allow a regular expression</span>
    <span>match</span><span>(</span><span>localvar</span><span>,</span> <span>"t"</span><span>);</span> <span># =&gt; 4, since the 't' is the fourth character</span>

    <span># Split on a delimiter</span>
    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo-bar-baz"</span><span>,</span> <span>arr</span><span>,</span> <span>"-"</span><span>);</span> <span># a[1] = "foo"; a[2] = "bar"; a[3] = "baz"; n = 3</span>

    <span># Other useful stuff</span>
    <span>sprintf</span><span>(</span><span>"%s %d %d %d"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "Testing 1 2 3"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "oob"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>4</span><span>);</span> <span># =&gt; "bar"</span>
    <span>length</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; 3</span>
    <span>tolower</span><span>(</span><span>"FOO"</span><span>);</span> <span># =&gt; "foo"</span>
    <span>toupper</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; "FOO"</span>
<span>}</span>

<span>function</span> <span>io_functions</span><span>(</span>    <span>localvar</span><span>)</span> <span>{</span>

    <span># You've already seen print</span>
    <span>print</span> <span>"Hello world"</span><span>;</span>

    <span># There's also printf</span>
    <span>printf</span><span>(</span><span>"%s %d %d %d\n"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span>

    <span># AWK doesn't have file handles, per se. It will automatically open a file</span>
    <span># handle for you when you use something that needs one. The string you used</span>
    <span># for this can be treated as a file handle, for purposes of I/O. This makes</span>
    <span># it feel sort of like shell scripting, but to get the same output, the string</span>
    <span># must match exactly, so use a variable:</span>

    <span>outfile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>

    <span>print</span> <span>"foobar"</span> <span>&gt;</span> <span>outfile</span><span>;</span>

    <span># Now the string outfile is a file handle. You can close it:</span>
    <span>close</span><span>(</span><span>outfile</span><span>);</span>

    <span># Here's how you run something in the shell</span>
    <span>system</span><span>(</span><span>"echo foobar"</span><span>);</span> <span># =&gt; prints foobar</span>

    <span># Reads a line from standard input and stores in localvar</span>
    <span>getline</span> <span>localvar</span><span>;</span>

    <span># Reads a line from a pipe (again, use a string so you close it properly)</span>
    <span>cmd</span> <span>=</span> <span>"echo foobar"</span><span>;</span>
    <span>cmd</span> <span>|</span> <span>getline</span> <span>localvar</span><span>;</span> <span># localvar =&gt; "foobar"</span>
    <span>close</span><span>(</span><span>cmd</span><span>);</span>

    <span># Reads a line from a file and stores in localvar</span>
    <span>infile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>
    <span>getline</span> <span>localvar</span> <span>&lt;</span> <span>infile</span><span>;</span> 
    <span>close</span><span>(</span><span>infile</span><span>);</span>
<span>}</span>

<span># As I said at the beginning, AWK programs consist of a collection of patterns</span>
<span># and actions. You've already seen the BEGIN pattern. Other</span>
<span># patterns are used only if you're processing lines from files or standard</span>
<span># input.</span>
<span>#</span>
<span># When you pass arguments to AWK, they are treated as file names to process.</span>
<span># It will process them all, in order. Think of it like an implicit for loop,</span>
<span># iterating over the lines in these files. these patterns and actions are like</span>
<span># switch statements inside the loop. </span>

<span>/^fo+bar$/</span> <span>{</span>

    <span># This action will execute for every line that matches the regular</span>
    <span># expression, /^fo+bar$/, and will be skipped for any line that fails to</span>
    <span># match it. Let's just print the line:</span>

    <span>print</span><span>;</span>

    <span># Whoa, no argument! That's because print has a default argument: $0.</span>
    <span># $0 is the name of the current line being processed. It is created</span>
    <span># automatically for you.</span>

    <span># You can probably guess there are other $ variables. Every line is</span>
    <span># implicitly split before every action is called, much like the shell</span>
    <span># does. And, like the shell, each field can be access with a dollar sign</span>

    <span># This will print the second and fourth fields in the line</span>
    <span>print</span> <span>$</span><span>2</span><span>,</span> <span>$</span><span>4</span><span>;</span>

    <span># AWK automatically defines many other variables to help you inspect and</span>
    <span># process each line. The most important one is NF</span>

    <span># Prints the number of fields on this line</span>
    <span>print</span> <span>NF</span><span>;</span>

    <span># Print the last field on this line</span>
    <span>print</span> <span>$</span><span>NF</span><span>;</span>
<span>}</span>

<span># Every pattern is actually a true/false test. The regular expression in the</span>
<span># last pattern is also a true/false test, but part of it was hidden. If you</span>
<span># don't give it a string to test, it will assume $0, the line that it's</span>
<span># currently processing. Thus, the complete version of it is this:</span>

<span>$</span><span>0</span> <span>~</span> <span>/^fo+bar$/</span> <span>{</span>
    <span>print</span> <span>"Equivalent to the last pattern"</span><span>;</span>
<span>}</span>

<span>a</span> <span>&gt;</span> <span>0</span> <span>{</span>
    <span># This will execute once for each line, as long as a is positive</span>
<span>}</span>

<span># You get the idea. Processing text files, reading in a line at a time, and</span>
<span># doing something with it, particularly splitting on a delimiter, is so common</span>
<span># in UNIX that AWK is a scripting language that does all of it for you, without</span>
<span># you needing to ask. All you have to do is write the patterns and actions</span>
<span># based on what you expect of the input, and what you want to do with it.</span>

<span># Here's a quick example of a simple script, the sort of thing AWK is perfect</span>
<span># for. It will read a name from standard input and then will print the average</span>
<span># age of everyone with that first name. Let's say you supply as an argument the</span>
<span># name of a this data file:</span>
<span>#</span>
<span># Bob Jones 32</span>
<span># Jane Doe 22</span>
<span># Steve Stevens 83</span>
<span># Bob Smith 29</span>
<span># Bob Barker 72</span>
<span>#</span>
<span># Here's the script:</span>

<span>BEGIN</span> <span>{</span>

    <span># First, ask the user for the name</span>
    <span>print</span> <span>"What name would you like the average age for?"</span><span>;</span>

    <span># Get a line from standard input, not from files on the command line</span>
    <span>getline</span> <span>name</span> <span>&lt;</span> <span>"/dev/stdin"</span><span>;</span>
<span>}</span>

<span># Now, match every line whose first field is the given name</span>
<span>$</span><span>1</span> <span>==</span> <span>name</span> <span>{</span>

    <span># Inside here, we have access to a number of useful variables, already</span>
    <span># pre-loaded for us:</span>
    <span># $0 is the entire line</span>
    <span># $3 is the third field, the age, which is what we're interested in here</span>
    <span># NF is the number of fields, which should be 3</span>
    <span># NR is the number of records (lines) seen so far</span>
    <span># FILENAME is the name of the file being processed</span>
    <span># FS is the field separator being used, which is " " here</span>
    <span># ...etc. There are plenty more, documented in the man page.</span>

    <span># Keep track of a running total and how many lines matched</span>
    <span>sum</span> <span>+=</span> <span>$</span><span>3</span><span>;</span>
    <span>nlines</span><span>++</span><span>;</span>
<span>}</span>

<span># Another special pattern is called END. It will run after processing all the</span>
<span># text files. Unlike BEGIN, it will only run if you've given it input to</span>
<span># process. It will run after all the files have been read and processed</span>
<span># according to the rules and actions you've provided. The purpose of it is</span>
<span># usually to output some kind of final report, or do something with the</span>
<span># aggregate of the data you've accumulated over the course of the script.</span>

<span>END</span> <span>{</span>
    <span>if</span> <span>(</span><span>nlines</span><span>)</span>
        <span>print</span> <span>"The average age for "</span> <span>name</span> <span>" is "</span> <span>sum</span> <span>/</span> <span>nlines</span><span>;</span>
<span>}</span>
</pre><p><span>&nbsp;</span></p></div>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43112/calling-variants-in-non-diploid-systems</guid>
	<pubDate>Sat, 26 Jun 2021 15:37:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43112/calling-variants-in-non-diploid-systems</link>
	<title><![CDATA[Calling variants in non-diploid systems]]></title>
	<description><![CDATA[<p><span>The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been accomplished on human mitochondrial&nbsp;</span><span>DNA</span><span>&nbsp;although the same approaches will work equally good on viral and bacterial genomes (</span><a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html#Rebolledo-Jaramillo2014">Rebolledo-Jaramillo&nbsp;<em>et al.</em>&nbsp;2014</a><span>,&nbsp;</span><a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html#Li2015">Li&nbsp;<em>et al.</em>&nbsp;2015</a><span>).</span></p><p>Address of the bookmark: <a href="https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html" rel="nofollow">https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/non-dip/tutorial.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

</channel>
</rss>