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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/34528?offset=430</link>
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	<description><![CDATA[]]></description>
	
	<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/37737/rebaler-program-for-conducting-reference-based-assemblies-using-long-reads</guid>
	<pubDate>Tue, 18 Sep 2018 07:52:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37737/rebaler-program-for-conducting-reference-based-assemblies-using-long-reads</link>
	<title><![CDATA[Rebaler: program for conducting reference-based assemblies using long reads.]]></title>
	<description><![CDATA[<p>Rebaler is a program for conducting reference-based assemblies using long reads. It relies mainly on&nbsp;<a href="https://github.com/lh3/minimap2">minimap2</a>&nbsp;for alignment and&nbsp;<a href="https://github.com/isovic/racon">Racon</a>&nbsp;for making consensus sequences.</p>
<p>I made Rebaler for bacterial genomes (specifically for the task of&nbsp;<a href="https://github.com/rrwick/Basecalling-comparison">testing basecallers</a>). It should in principle work for non-bacterial genomes as well, but I haven't tested it.</p><p>Address of the bookmark: <a href="https://github.com/rrwick/Rebaler" rel="nofollow">https://github.com/rrwick/Rebaler</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37962/wtdbg2-a-de-novo-sequence-assembler-for-long-noisy-reads-produced-by-pacbio-or-oxford-nanopore</guid>
	<pubDate>Fri, 19 Oct 2018 08:48:43 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37962/wtdbg2-a-de-novo-sequence-assembler-for-long-noisy-reads-produced-by-pacbio-or-oxford-nanopore</link>
	<title><![CDATA[Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore]]></title>
	<description><![CDATA[<p><span>Wtdbg2 is a&nbsp;</span><em>de novo</em><span>&nbsp;sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb&nbsp;</span><a href="https://www.nature.com/articles/nature25458">Axolotl</a><span>&nbsp;genome at a speed tens of times faster than&nbsp;</span><a href="https://github.com/marbl/canu">CANU</a><span>&nbsp;and&nbsp;</span><a href="https://github.com/PacificBiosciences/FALCON">FALCON</a><span>while producing contigs of comparable base accuracy.</span></p><p>Address of the bookmark: <a href="https://github.com/ruanjue/wtdbg2" rel="nofollow">https://github.com/ruanjue/wtdbg2</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40701/fastgt-an-alignment-free-method-for-calling-common-snvs-directly-from-raw-sequencing-reads</guid>
	<pubDate>Tue, 28 Jan 2020 03:27:33 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40701/fastgt-an-alignment-free-method-for-calling-common-snvs-directly-from-raw-sequencing-reads</link>
	<title><![CDATA[FastGT: an alignment-free method for calling common SNVs directly from raw sequencing reads]]></title>
	<description><![CDATA[<p>FastGT is a program package for whole-genome genotyping of genome variants directly from raw sequencing reads. It is written in C and runs in Linux. FastGT uses a list of variant-specific k-mer pairs that are unique in human genome, counts the frequency of k-mers in sequencing data and predicts the genotype. All this takes less than 1 hour on average low-cost Linux server.</p>
<p><a href="http://bioinfo.ut.ee/FastGT/">http://bioinfo.ut.ee/FastGT/</a></p>
<p><strong><a href="https://github.com/bioinfo-ut/GenomeTester4/">https://github.com/bioinfo-ut/GenomeTester4/</a></strong></p><p>Address of the bookmark: <a href="http://bioinfo.ut.ee/FastGT/" rel="nofollow">http://bioinfo.ut.ee/FastGT/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
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	<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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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads</guid>
	<pubDate>Sun, 14 Mar 2021 09:42:47 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42946/aligngraph2-similar-genome-assisted-reassembly-pipeline-for-pacbio-long-reads</link>
	<title><![CDATA[AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads]]></title>
	<description><![CDATA[<p><span>AlignGraph2 is the second version of&nbsp;</span><a href="https://github.com/baoe/AlignGraph">AlignGraph</a><span>&nbsp;for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome.</span></p>
<p><span>More at&nbsp;https://academic.oup.com/bib/advance-article-abstract/doi/10.1093/bib/bbab022/6146772</span></p><p>Address of the bookmark: <a href="https://github.com/huangs001/AlignGraph2" rel="nofollow">https://github.com/huangs001/AlignGraph2</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
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	<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/27080/mrfast-micro-read-fast-alignment-search-tool</guid>
	<pubDate>Tue, 26 Apr 2016 03:50:06 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27080/mrfast-micro-read-fast-alignment-search-tool</link>
	<title><![CDATA[mrFAST:  Micro Read Fast Alignment Search Tool]]></title>
	<description><![CDATA[<p><span>mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 4+4 bp. This manual, describes how to choose the parameters and tune mrFAST with respect to the library settings. mrFAST is designed to find&nbsp;</span><strong><span style="text-decoration: underline;">'all'</span></strong><span>&nbsp; mappings for a given set of reads, however it can return one "best" map location if the relevant parameter is invoked.</span></p>
<p><span>More at&nbsp;http://mrfast.sourceforge.net/manual.html</span></p><p>Address of the bookmark: <a href="http://mrfast.sourceforge.net/manual.html" rel="nofollow">http://mrfast.sourceforge.net/manual.html</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30555/yaha</guid>
	<pubDate>Fri, 20 Jan 2017 05:38:05 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30555/yaha</link>
	<title><![CDATA[YAHA]]></title>
	<description><![CDATA[<p>YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments. Unlike other aligners that report all, or one, alignment per query, or that use simple heuristics to select alignments, YAHA uses a directed acyclic graph to find the optimal set of alignments that cover a query using a biologically relevant breakpoint penalty. YAHA can also report multiple mappings per defined segment of the query. We show that YAHA detects more breakpoints in less time than BWA-SW across all SV classes, and especially excels at complex SVs comprising multiple breakpoints.</p>
<p><strong>Availability:</strong> YAHA is currently supported on 64-bit Linux systems. Binaries and sample data are freely available for download from <a href="http://faculty.virginia.edu/irahall/YAHA" target="pmc_ext">http://faculty.virginia.edu/irahall/YAHA</a>.</p>
<p><strong>Contact:</strong></p>
<p>http://genome.wustl.edu/people/groups/detail/hall-lab/</p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463118/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3463118/</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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