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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/38735?offset=540</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/36630/frequent-paired-end-reads-pe-2x100-mapping-command-lines</guid>
	<pubDate>Tue, 15 May 2018 08:59:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/36630/frequent-paired-end-reads-pe-2x100-mapping-command-lines</link>
	<title><![CDATA[Frequent Paired-end reads (PE 2x100) mapping command lines]]></title>
	<description><![CDATA[
<p>bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam  </p>

<p>bwa aln hs37m.fa r1.fq &gt; r1.sai &amp;&amp; bwa aln hs37m.fa r2.fq &gt; r2.sai \  <br />    &amp;&amp; bwa sampe hs37m r1.sai r2.sai r1.fq r2.fq &gt; r12.bwa.sam  </p>

<p>bwa bwasw ../index/bwa/hs37m.fa r12.fq &gt; r12.bwasw.sam  </p>

<p>gsnap -A sam -d hs37m r1.fq r2.fq &gt; r12.gsnap.sam  </p>

<p>novoalign -r Random -o SAM -f r1.fq r2.fq -i 500 50 -d hs37m-k14s3.novo &gt; r12.novo.sam  </p>

<p>smalt map -f samsoft -i 650 -o r12.smalt-k20s13.sam hs37m-k20s13 r1.fq r2.fq  </p>

<p>stampy.py -g hs37m -h hs37m -o r12.stampy.sam -M r1.fq,r2.fq  </p>

<p>soap -D hs37m.fa.index -a r1.fq -b r2.fq -l 32 -g 3 -u dummy -2 dummy -o r12.soap</p>
]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36895/npscarf-real-time-scaffolder-using-spades-contigs-and-nanopore-sequencing-reads</guid>
	<pubDate>Mon, 11 Jun 2018 05:14:57 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36895/npscarf-real-time-scaffolder-using-spades-contigs-and-nanopore-sequencing-reads</link>
	<title><![CDATA[npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads]]></title>
	<description><![CDATA[npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple structural analyses such as gene ordering, plasmid forming.<p>Address of the bookmark: <a href="http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html" rel="nofollow">http://japsa.readthedocs.io/en/latest/tools/jsa.np.npscarf.html</a></p>]]></description>
	<dc:creator>Shruti Paniwala</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>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41030/slr-superscaffolder-a-scaffold-assemble-pipeline-for-stlfr-reads</guid>
	<pubDate>Fri, 14 Feb 2020 14:23:30 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41030/slr-superscaffolder-a-scaffold-assemble-pipeline-for-stlfr-reads</link>
	<title><![CDATA[SLR-superscaffolder: A scaffold assemble pipeline for stLFR reads.]]></title>
	<description><![CDATA[<p>This is a scaffold assembler designed for stLFR reads[1]. It uses the link-reads information from stLFR reads to assemble contigs to scaffolds.</p>
<p>Here is an illustration of this pipeline:</p>
<p>&nbsp;<img src="https://github.com/BGI-Qingdao/SLR-superscaffolder/raw/master/image.png" alt="image" style="border: 0px;"></p><p>Address of the bookmark: <a href="https://github.com/BGI-Qingdao/SLR-superscaffolder" rel="nofollow">https://github.com/BGI-Qingdao/SLR-superscaffolder</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42477/hifiasm-a-haplotype-resolved-assembler-for-accurate-hifi-reads</guid>
	<pubDate>Thu, 24 Dec 2020 10:03:36 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42477/hifiasm-a-haplotype-resolved-assembler-for-accurate-hifi-reads</link>
	<title><![CDATA[Hifiasm: a haplotype-resolved assembler for accurate Hifi reads]]></title>
	<description><![CDATA[<p><span>Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. It can assemble a human genome in several hours and works with the California redwood genome, one of the most complex genomes sequenced so far. Hifiasm can produce primary/alternate assemblies of quality competitive with the best assemblers. It also introduces a new graph binning algorithm and achieves the best haplotype-resolved assembly given trio data.</span></p><p>Address of the bookmark: <a href="https://github.com/chhylp123/hifiasm" rel="nofollow">https://github.com/chhylp123/hifiasm</a></p>]]></description>
	<dc:creator>Jit</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/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/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines</guid>
	<pubDate>Wed, 15 Jun 2016 17:18:36 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27839/lorma-a-tool-for-correcting-sequencing-errors-in-long-reads-such-those-produced-by-pacific-biosciences-sequencing-machines</link>
	<title><![CDATA[LoRMA: a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines]]></title>
	<description><![CDATA[<p>LoRMA is a tool for correcting sequencing errors in long reads such those produced by Pacific Biosciences sequencing machines.</p>
<p>Publication:</p>
<ul>
<li>L. Salmela, R. Walve, E. Rivals, and E. Ukkonen: Accurate selfcorrection of errors in long reads using de Bruijn graphs. Accepted to RECOMB-Seq 2016.</li>
</ul>
<p>Download:</p>
<ul>
<li><a href="https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/LoRMA-0.3.tar.gz">LoRMA 0.3 source files</a></li>
<li><a href="https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/README.txt">README</a></li>
</ul><p>Address of the bookmark: <a href="https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/" rel="nofollow">https://www.cs.helsinki.fi/u/lmsalmel/LoRMA/</a></p>]]></description>
	<dc:creator>Jit</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>

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