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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/39671?offset=220</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37241/remilo-reference-assisted-misassembly-detection-algorithm-using-short-and-long-reads</guid>
	<pubDate>Fri, 06 Jul 2018 04:27:49 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37241/remilo-reference-assisted-misassembly-detection-algorithm-using-short-and-long-reads</link>
	<title><![CDATA[ReMILO: reference assisted misassembly detection algorithm using short and long reads.]]></title>
	<description><![CDATA[ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to detect misassemblies. In addition, ReMILO also aligns the contigs to long reads and find their differences from the long reads to detect more misassemblies.<p>Address of the bookmark: <a href="https://github.com/songc001/remilo" rel="nofollow">https://github.com/songc001/remilo</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/38199/pacasus-correction-of-palindromes-in-long-reads-from-pacbio-and-nanopore</guid>
	<pubDate>Mon, 12 Nov 2018 05:26:48 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38199/pacasus-correction-of-palindromes-in-long-reads-from-pacbio-and-nanopore</link>
	<title><![CDATA[Pacasus: Correction of palindromes in long reads from PacBio and Nanopore]]></title>
	<description><![CDATA[<p><br>Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification. Check the poster from the Revolutionizing Next-Generation Sequencing (2nd edition) conference in the source folder:&nbsp;<a href="https://github.com/swarris/Pacasus/blob/master/vib2017.pdf">https://github.com/swarris/Pacasus/blob/master/vib2017.pdf</a>.</p>
<p>The prepint version is found on&nbsp;<a href="http://www.biorxiv.org/content/early/2017/08/09/173872">http://www.biorxiv.org/content/early/2017/08/09/173872</a></p>
<p>It uses the pyPaSWAS framework for sequence alignment (<a href="https://github.com/swarris/pyPaSWAS">https://github.com/swarris/pyPaSWAS</a>)</p><p>Address of the bookmark: <a href="https://github.com/swarris/Pacasus" rel="nofollow">https://github.com/swarris/Pacasus</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/file/view/38886/evaluation-of-genome-assembly-software-based-on-long-reads</guid>
	<pubDate>Fri, 01 Feb 2019 11:55:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/file/view/38886/evaluation-of-genome-assembly-software-based-on-long-reads</link>
	<title><![CDATA[Evaluation of genome assembly software based on long reads]]></title>
	<description><![CDATA[<p>TGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence diversity. They have also been applied to resequencing analyses, to create detailed maps of structural variations in many species. Also, these new technologies have been used to fill in many of the gaps in the human reference genome.</p><p>In this report, we compare and evaluate several genome assembly software based on TSG technology. The experimentation has been performed on 4 reference genomes and the results evaluated with the QUAST software. The 11 software that have been evaluated are: Celera Assembler , Falcon , Miniasm, Newbler , SGA Assembler, Smartdenovo, Abruijn, Ra, DBG2OLC, Spades and Cerulean. The first 8 software use only long reads, while the 3 last software can merge long and short reads</p>]]></description>
	<dc:creator>BioStar</dc:creator>
	<enclosure url="https://bioinformaticsonline.com/file/download/38886" length="382699" type="application/pdf" />
</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/42132/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins</guid>
	<pubDate>Mon, 17 Aug 2020 05:25:10 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42132/squeezemeta-a-fully-automated-metagenomics-pipeline-from-reads-to-bins</link>
	<title><![CDATA[SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins]]></title>
	<description><![CDATA[<p>SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. Thus, SqueezeMeta features several unique characteristics:</p>
<ol>
<li>Co-assembly procedure with read mapping for estimation of the abundances of genes in each metagenome</li>
<li>Co-assembly of a large number of metagenomes via merging of individual metagenomes</li>
<li>Includes binning and bin checking, for retrieving individual genomes</li>
<li>The results are stored in a database, where they can be easily exported and shared, and can be inspected anywhere using a web interface.</li>
<li>Internal checks for the assembly and binning steps inform about the consistency of contigs and bins, allowing to spot potential chimeras.</li>
<li>Metatranscriptomic support via mapping of cDNA reads against reference metagenomes</li>
</ol><p>Address of the bookmark: <a href="https://github.com/jtamames/SqueezeMeta" rel="nofollow">https://github.com/jtamames/SqueezeMeta</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly</guid>
	<pubDate>Tue, 17 Aug 2021 13:17:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43260/bioinformatics-tools-for-telomere-to-telomere-assembly</link>
	<title><![CDATA[Bioinformatics tools for telomere to telomere assembly !]]></title>
	<description><![CDATA[<p>●&nbsp;<a href="https://github.com/arangrhie/merfin" target="_blank">Merfin</a>&nbsp;&ndash; k-mer-based assembly and variant calling evaluation for improved consensus accuracy (Arang Rhie)<br />●&nbsp;<a href="https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1" target="_blank">PanGenie</a>&nbsp;&ndash; algorithm that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation (Tobias Marschall)<br />●&nbsp;<a href="https://github.com/ConesaLab/SQANTI3" target="_blank">SQANTI3</a>&nbsp;&ndash; an automated pipeline for the classification of long-read transcripts that can assess the quality of data and the preprocessing pipeline (Roc&iacute;o Amor&iacute;n de Heged&uuml;s&nbsp;<a href="https://twitter.com/rocioadh" target="_blank">@rocioadh</a>)<br />●&nbsp;<a href="https://github.com/GenomeRIK/tama" target="_blank">tama</a>&nbsp;(Transcriptome Annotation by Modular Algorithms) &ndash; software designed for processing Iso-Seq data and other long-read transcriptome data (Richard Kuo&nbsp;<a href="https://twitter.com/GenomeRIK" target="_blank">@GenomeRIK</a>)<br />●&nbsp;<a href="https://github.com/PacificBiosciences/pbAA" target="_blank">pbaa</a>&nbsp;(PacBio Amplicon Analysis) &ndash; separates complex mixtures of amplicon targets from genomic samples to cluster and generate high-quality consensus sequences from HiFi reads (Zev Kronenberg&nbsp;<a href="https://twitter.com/zevkronenberg" target="_blank">@zevkronenberg</a>)<br />●&nbsp;<a href="https://github.com/yuanyuan929/bellerophon" target="_blank">bellerophon</a>&nbsp;&ndash; analyzes MHC typing and other low-complexity gene amplicon data; performs allele calling while detecting polymorphic sites within the sequences and removing potential chimeric sequence variants (Yuanyuan Cheng&nbsp;<a href="https://twitter.com/Yuanyuan929" target="_blank">@Yuanyuan929</a>)<br />●&nbsp;<a href="https://github.com/amwenger/svpack" target="_blank">svpack</a>&nbsp;&ndash; tools for filtering, comparing, and annotating structural variant (SV) calls in VCF format (Aaron Wenger)<br />●&nbsp;<a href="https://github.com/AntonBankevich/jumboDB" target="_blank">JumboDB</a>&nbsp;&ndash; tool for de Bruijn graph construction (Anton Bankevich&nbsp;<a href="https://twitter.com/AntonBankevich" target="_blank">@AntonBankevich</a>)<br />●&nbsp;<a href="https://github.com/ksahlin/ultra" target="_blank">uLTRA</a>&nbsp;&ndash; tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. (Kristoffer Sahlin&nbsp;<a href="https://twitter.com/krsahlin" target="_blank">@krsahlin</a>)<br />●&nbsp;<a href="https://www.biorxiv.org/content/10.1101/2021.01.25.428044v1.full.pdf" target="_blank">LeafGo</a>&nbsp;&ndash; workflow to rapidly produce high-quality de novo plant genomes (Luca Ermini&nbsp;<a href="https://twitter.com/ermini_luca" target="_blank">@ermini_luca</a>)</p><p>Reference:</p><p>https://www.pacb.com/blog/young-investigators-share-stellar-science-career-advice-and-bioinformatics-tools-at-smrt-leiden-2021/</p><p>&nbsp;</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/26911/raca-reference-assisted-chromosome-assembly</guid>
	<pubDate>Wed, 06 Apr 2016 09:29:50 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26911/raca-reference-assisted-chromosome-assembly</link>
	<title><![CDATA[RACA: Reference-Assisted Chromosome Assembly]]></title>
	<description><![CDATA[<p>Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads.</p>
<p>http://www.ncbi.nlm.nih.gov/pubmed/23307812</p>
<p>http://bioen-compbio.bioen.illinois.edu/RACA/</p><p>Address of the bookmark: <a href="http://bioen-compbio.bioen.illinois.edu/RACA/" rel="nofollow">http://bioen-compbio.bioen.illinois.edu/RACA/</a></p>]]></description>
	<dc:creator>Priya Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27261/segemehl</guid>
	<pubDate>Tue, 10 May 2016 08:10:15 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27261/segemehl</link>
	<title><![CDATA[segemehl]]></title>
	<description><![CDATA[<p><span>segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map&nbsp;primer- or polyadenylation contaminated reads correctly.&nbsp; segemehl implements a matching strategy based on enhanced suffix arrays (ESA).&nbsp;</span></p>
<p><span>More at&nbsp;http://www.bioinf.uni-leipzig.de/Software/segemehl/</span></p>
<p><span>Manual&nbsp;http://www.bioinf.uni-leipzig.de/Software/segemehl/segemehl_manual_0_1_7.pdf</span></p><p>Address of the bookmark: <a href="http://hoffmann.bioinf.uni-leipzig.de/LIFE/segemehl.html" rel="nofollow">http://hoffmann.bioinf.uni-leipzig.de/LIFE/segemehl.html</a></p>]]></description>
	<dc:creator>Anjana</dc:creator>
</item>

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