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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/37957?offset=470</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</guid>
	<pubDate>Mon, 30 Apr 2018 04:38:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</link>
	<title><![CDATA[ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.]]></title>
	<description><![CDATA[<p><span>ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.&nbsp;</span></p>
<p><span>Detail paper at&nbsp;https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8</span></p><p>Address of the bookmark: <a href="https://github.com/VicugnaPacos/ALPACA" rel="nofollow">https://github.com/VicugnaPacos/ALPACA</a></p>]]></description>
	<dc:creator>Seema Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36635/circlator-automated-circularization-of-genome-assemblies-using-long-sequencing-reads</guid>
	<pubDate>Tue, 15 May 2018 09:42:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36635/circlator-automated-circularization-of-genome-assemblies-using-long-sequencing-reads</link>
	<title><![CDATA[Circlator: automated circularization of genome assemblies using long sequencing reads]]></title>
	<description><![CDATA[A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. 

Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0. PMID: 26714481.<p>Address of the bookmark: <a href="http://sanger-pathogens.github.io/circlator/" rel="nofollow">http://sanger-pathogens.github.io/circlator/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36921/breakpointer-using-local-mapping-artifacts-to-support-sequence-breakpoint-discovery-from-single-end-reads</guid>
	<pubDate>Tue, 12 Jun 2018 12:41:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36921/breakpointer-using-local-mapping-artifacts-to-support-sequence-breakpoint-discovery-from-single-end-reads</link>
	<title><![CDATA[Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads]]></title>
	<description><![CDATA[Breakpointer is a fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs).<p>Address of the bookmark: <a href="https://github.com/ruping/Breakpointer" rel="nofollow">https://github.com/ruping/Breakpointer</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37759/pandaseq-is-a-program-to-align-illumina-reads-optionally-with-pcr-primers-embedded-in-the-sequence-and-reconstruct-an-overlapping-sequence</guid>
	<pubDate>Fri, 21 Sep 2018 10:19:52 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37759/pandaseq-is-a-program-to-align-illumina-reads-optionally-with-pcr-primers-embedded-in-the-sequence-and-reconstruct-an-overlapping-sequence</link>
	<title><![CDATA[PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.]]></title>
	<description><![CDATA[<p>Development packages for zlib and libbz2 are needed, as well as a standard compiler environment. On Ubuntu, this can be installed via:</p>
<pre><code>sudo apt-get install build-essential libtool automake zlib1g-dev libbz2-dev pkg-config
</code></pre>
<p>On MacOS, the Apple Developer tools and Fink (or MacPorts or Brew) must be installed, then:</p>
<pre><code>sudo fink install bzip2-dev pkgconfig</code></pre><p>Address of the bookmark: <a href="https://github.com/neufeld/pandaseq" rel="nofollow">https://github.com/neufeld/pandaseq</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40460/sviper-swipe-your-structural-variants-called-on-long-ontpacbio-reads-with-short-exact-illumina-reads</guid>
	<pubDate>Sun, 22 Dec 2019 03:48:28 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40460/sviper-swipe-your-structural-variants-called-on-long-ontpacbio-reads-with-short-exact-illumina-reads</link>
	<title><![CDATA[SViper: Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.]]></title>
	<description><![CDATA[<p>Call sviper</p>
<pre><code>~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants
</code></pre>
<p>This will output a&nbsp;<code>polished_variants.vcf</code>&nbsp;file, that contains all the refined variants.</p>
<p>Sometimes it is helpful to look at the polished sequence, e.g. with the IGV browser. In that case you want SViper to output the polished and aligned sequences in a bam file via the option&nbsp;<code>--output-polished-bam</code>:</p>
<pre><code>~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants --output-</code>polished-bam</pre><p>Address of the bookmark: <a href="https://github.com/smehringer/SViper" rel="nofollow">https://github.com/smehringer/SViper</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40972/deepbinner-a-signal-level-demultiplexer-for-oxford-nanopore-reads</guid>
	<pubDate>Mon, 10 Feb 2020 02:45:53 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40972/deepbinner-a-signal-level-demultiplexer-for-oxford-nanopore-reads</link>
	<title><![CDATA[Deepbinner: a signal-level demultiplexer for Oxford Nanopore reads]]></title>
	<description><![CDATA[<p>Deepbinner is a tool for demultiplexing barcoded <a href="https://nanoporetech.com/">Oxford Nanopore</a> sequencing reads. It does this with a deep <a href="https://adeshpande3.github.io/adeshpande3.github.io/A-Beginner's-Guide-To-Understanding-Convolutional-Neural-Networks/">convolutional neural network</a> classifier, using many of the <a href="https://towardsdatascience.com/neural-network-architectures-156e5bad51ba">architectural advances</a> that have proven successful in image classification. Unlike other demultiplexers (e.g. Albacore and <a href="https://github.com/rrwick/Porechop">Porechop</a>), Deepbinner identifies barcodes from the raw signal (a.k.a. squiggle) which gives it greater sensitivity and fewer unclassified reads.</p><p>Address of the bookmark: <a href="https://github.com/rrwick/Deepbinner" rel="nofollow">https://github.com/rrwick/Deepbinner</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</guid>
	<pubDate>Mon, 17 Aug 2020 05:21:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</link>
	<title><![CDATA[SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis]]></title>
	<description><![CDATA[<p><span>SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, &hellip;).</span><br><span>The bioinformatics treatment is based on Vsearch [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/27781170">Rognes 2016</a><span>] which showed to be both accurate and fast [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/26664811">Wescott 2015</a><span>].The statistical analysis is based on DESeq2 R package [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/20979621">Anders and Huber 2010</a><span>] which robustly identifies the differential abundant features as suggested in [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/">McMurdie and Holmes 2014</a><span>] and [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/">Jonsson2016</a><span>]. SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/25516281">Love 2014</a><span>].</span><br><span>SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and figures can be downloaded in several formats. A presentation about SHAMAN is available&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_presentation.pdf">here</a><span>&nbsp;and a poster&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_poster.pdf">here</a><span>.&nbsp;</span></p>
<p><span>More at&nbsp;<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4</a></span></p><p>Address of the bookmark: <a href="https://github.com/aghozlane/shaman" rel="nofollow">https://github.com/aghozlane/shaman</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</guid>
	<pubDate>Thu, 09 Mar 2023 02:56:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44234/steps-to-find-palindrome-in-genomes</link>
	<title><![CDATA[Steps to find palindrome in genomes !]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Palindromes are sequences of nucleotides that read the same backward as forward. They can be present in genomes and have various biological functions. Here are some methods for discovering palindromes in genomes:</p><ol>
<li>
<p>Direct sequence search: One of the simplest ways to discover palindromes is to search the genome sequence directly for palindromic sequences using pattern matching tools, such as regular expressions or string algorithms. This approach can be useful for discovering simple palindromes, but may miss more complex palindromic structures.</p>
</li>
<li>
<p>Dot plot analysis: Dot plot analysis is a graphical method that can be used to identify palindromic regions in a genome. It involves plotting the genome sequence against itself and examining the diagonal patterns that emerge. Palindromic regions will appear as symmetrical patterns along the diagonal.</p>
</li>
<li>
<p>Restriction enzyme analysis: Some restriction enzymes, such as EcoRI and HindIII, recognize palindromic sequences and cleave DNA at these sites. By digesting the genome with these enzymes and examining the resulting fragments, palindromic regions can be identified.</p>
</li>
<li>
<p>Next-generation sequencing: High-throughput sequencing technologies, such as PacBio and Oxford Nanopore, can generate long reads that can span entire palindromic regions. By mapping these reads to the genome, palindromic regions can be identified and characterized.</p>
</li>
<li>
<p>Comparative genomics: Comparing the genomes of related species can also reveal palindromic regions that are conserved across evolutionarily divergent lineages. This approach can help identify functional palindromes that are under selective pressure.</p>
</li>
</ol><p>Overall, the discovery of palindromic sequences in genomes can be accomplished using a variety of methods, each with their own advantages and limitations. A combination of these methods can provide a comprehensive understanding of the palindromic landscape of a genome.</p></div></div></div></div></div></div></div></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27841/covcal-coverage-read-count-calculator</guid>
	<pubDate>Wed, 15 Jun 2016 18:08:13 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27841/covcal-coverage-read-count-calculator</link>
	<title><![CDATA[CovCal: Coverage / Read Count Calculator]]></title>
	<description><![CDATA[<h2>Coverage / Read Count Calculator</h2>
<h4>Calculate how much sequencing you need to hit a target depth of coverage (or vice versa).</h4>
<p><span>Instructions:</span> set the read length/configuration and genome size, then select what you want to calculate.</p>
<p>Written by <a href="http://stephenturner.us/" target="blank">Stephen Turner</a>, based on the <a href="http://www.ncbi.nlm.nih.gov/pubmed/3294162" target="_blank">Lander-Waterman formula</a>, inspired by <a href="http://core-genomics.blogspot.com/2016/05/how-many-reads-to-sequence-genome.html" target="_blank">a similar calculator</a> written by James Hadfield. Coverage is calculated as <em>C=LN/G</em> and reads as <em>N=CG/L</em> where <em>C</em> = Coverage (X),<em>L</em> = Read length (bp), <em>G</em> = Haploid genome size (bp), and <em>N</em> = Number of reads. Source code <a href="https://github.com/stephenturner/covcalc" target="_blank">on GitHub</a>.</p><p>Address of the bookmark: <a href="http://apps.bioconnector.virginia.edu/covcalc/" rel="nofollow">http://apps.bioconnector.virginia.edu/covcalc/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34235/quorum-an-error-corrector-for-illumina-reads</guid>
	<pubDate>Wed, 08 Nov 2017 11:40:41 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34235/quorum-an-error-corrector-for-illumina-reads</link>
	<title><![CDATA[QuorUM: An Error Corrector for Illumina Reads]]></title>
	<description><![CDATA[<p><span><span>Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 &times; coverage Illumina data on average has an error in some read at every base in the genome. These errors make handling the data more complicated because they result in a large number of low-count erroneous&nbsp;</span><em>k</em><span>-mers in the reads. However, there is enough information in the reads to correct most of the sequencing errors, thus making subsequent use of the data (e.g. for mapping or assembly) easier. Here we use the term &ldquo;error correction&rdquo; to denote the reduction in errors due to both changes in individual bases and trimming of unusable sequence. We developed an error correction software called QuorUM. QuorUM is mainly aimed at error correcting Illumina reads for subsequent assembly. It is designed around the novel idea of minimizing the number of distinct erroneous&nbsp;</span><em>k</em><span>-mers in the output reads and preserving the most true&nbsp;</span><em>k</em><span>-mers, and we introduce a composite statistic &pi; that measures how successful we are at achieving this dual goal. We evaluate the performance of QuorUM by correcting actual Illumina reads from genomes for which a reference assembly is available.</span></span></p>
<p><span>QuorUM is distributed as an independent software package and as a module of the MaSuRCA assembly software. Both are available under the GPL open source license at&nbsp;</span><a href="http://www.genome.umd.edu/">http://www.genome.umd.edu</a><span>.</span></p><p>Address of the bookmark: <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130821" rel="nofollow">http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130821</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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