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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/42946?offset=190</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</guid>
	<pubDate>Tue, 08 May 2018 04:27:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</link>
	<title><![CDATA[HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads]]></title>
	<description><![CDATA[<p><strong>HISAT2</strong><span>&nbsp;is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs&nbsp;</span><a href="http://dl.acm.org/citation.cfm?id=2674828">[Sir&eacute;n et al. 2014]</a><span>, we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).&nbsp;</span></p>
<p><span>more at&nbsp;https://ccb.jhu.edu/software/hisat2/index.shtml</span></p><p>Address of the bookmark: <a href="https://github.com/infphilo/hisat2" rel="nofollow">https://github.com/infphilo/hisat2</a></p>]]></description>
	<dc:creator>Rahul Nayak</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/36918/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads</guid>
	<pubDate>Tue, 12 Jun 2018 08:14:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36918/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads</link>
	<title><![CDATA[P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads]]></title>
	<description><![CDATA[P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs.<p>Address of the bookmark: <a href="http://www.fishbrowser.org/software/P_RNA_scaffolder/" rel="nofollow">http://www.fishbrowser.org/software/P_RNA_scaffolder/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share</guid>
	<pubDate>Tue, 07 Aug 2018 04:41:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share</link>
	<title><![CDATA[AlignQC: A tool for assessing an alignment, and generating reports that are easy to share]]></title>
	<description><![CDATA[<p><span>Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.</span></p>
<p>https://f1000research.com/articles/6-100/</p>
<p>https://github.com/jason-weirather/AlignQC</p><p>Address of the bookmark: <a href="https://www.healthcare.uiowa.edu/labs/au/AlignQC/" rel="nofollow">https://www.healthcare.uiowa.edu/labs/au/AlignQC/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37840/long-read-assembly-workshop</guid>
	<pubDate>Thu, 04 Oct 2018 17:23:18 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37840/long-read-assembly-workshop</link>
	<title><![CDATA[Long read assembly workshop !]]></title>
	<description><![CDATA[<p>This is a tutorial for a workshop on long-read (PacBio) genome assembly.</p>
<p>It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data.</p>
<p>&nbsp;Please comment if you know any other long read addembly tutorial.</p><p>Address of the bookmark: <a href="http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly_v2/" rel="nofollow">http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly_v2/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39213/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads</guid>
	<pubDate>Tue, 02 Apr 2019 21:54:55 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39213/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads</link>
	<title><![CDATA[Flye: Fast and accurate de novo assembler for single molecule sequencing reads]]></title>
	<description><![CDATA[<p><span>Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.</span></p><p>Address of the bookmark: <a href="https://github.com/fenderglass/Flye" rel="nofollow">https://github.com/fenderglass/Flye</a></p>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40946/free-genomics-data</guid>
	<pubDate>Fri, 07 Feb 2020 14:08:31 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40946/free-genomics-data</link>
	<title><![CDATA[Free Genomics data !]]></title>
	<description><![CDATA[<p><span>The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane McCarthy) and colleagues in Pacific Biosciences (Jonas Korlach).</span></p>
<p><a href="https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/">https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/</a></p><p>Address of the bookmark: <a href="https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/" rel="nofollow">https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/</a></p>]]></description>
	<dc:creator>BioStar</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>
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<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>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27035/spades</guid>
	<pubDate>Tue, 19 Apr 2016 08:37:08 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27035/spades</link>
	<title><![CDATA[SPAdes]]></title>
	<description><![CDATA[<p>SPAdes &ndash; St. Petersburg genome assembler &ndash; is intended for both standard isolates and single-cell MDA bacteria assemblies. This manual will help you to install and run SPAdes. SPAdes version 3.7.1 was released under GPLv2 on March 8, 2016 and can be downloaded from <a href="http://bioinf.spbau.ru/en/spades" target="_blank">http://bioinf.spbau.ru/en/spades</a>.</p>
<p>Manual at http://spades.bioinf.spbau.ru/release3.7.1/manual.html</p><p>Address of the bookmark: <a href="http://bioinf.spbau.ru/spades" rel="nofollow">http://bioinf.spbau.ru/spades</a></p>]]></description>
	<dc:creator>Abhimanyu Singh</dc:creator>
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