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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/43254?offset=80</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/39671/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads</guid>
	<pubDate>Sat, 06 Jul 2019 03:48:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/39671/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>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases</guid>
	<pubDate>Wed, 12 Feb 2020 01:16:29 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases</link>
	<title><![CDATA[Biological databases !]]></title>
	<description><![CDATA[<p>Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...</p>
<p>ftp://ftp.ncbi.nih.gov/genomes/</p>
<p>https://hgdownload.soe.ucsc.edu/downloads.html</p><p>Address of the bookmark: <a href="ftp://ftp.ncbi.nih.gov/genomes/" rel="nofollow">ftp://ftp.ncbi.nih.gov/genomes/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads</guid>
	<pubDate>Mon, 04 May 2020 02:04:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41599/haslr-a-hybrid-assembler-which-uses-both-second-and-third-generation-sequencing-reads</link>
	<title><![CDATA[HASLR: a hybrid assembler which uses both second and third generation sequencing reads]]></title>
	<description><![CDATA[<p><span>HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of misassemblies on all the samples compared to other tested assemblers. Furthermore, the generated assemblies in terms of contiguity and accuracy are on par with the other tools on most of the samples. Availability. HASLR is an open source tool available at https://github.com/vpc-ccg/haslr.</span></p><p>Address of the bookmark: <a href="https://github.com/vpc-ccg/haslr" rel="nofollow">https://github.com/vpc-ccg/haslr</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/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/29614/art-set-of-simulation-tools</guid>
	<pubDate>Thu, 03 Nov 2016 08:28:25 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/29614/art-set-of-simulation-tools</link>
	<title><![CDATA[ART: Set of Simulation Tools]]></title>
	<description><![CDATA[<p>ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to test or benchmark a variety of method or tools for next-generation sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the simulation study of the <span><a href="http://www.1000genomes.org/" target="_blank">1000 Genomes Project<span></span></a></span> . ART is implemented in C++ with optimized algorithms and is highly efficient in read simulation. ART outputs reads in the FASTQ format, and alignments in the ALN format. ART can also generate alignments in the SAM alignment or UCSC BED file format. ART can be used together with genome variants simulators (e.g. <span><a href="http://bioinform.github.io/varsim/" target="_blank">VarSim<span></span></a></span>) for evaluating variant calling tools or methods.</p><p>Address of the bookmark: <a href="http://www.niehs.nih.gov/research/resources/software/biostatistics/art/" rel="nofollow">http://www.niehs.nih.gov/research/resources/software/biostatistics/art/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/30557/speedseq</guid>
	<pubDate>Fri, 20 Jan 2017 06:05:43 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/30557/speedseq</link>
	<title><![CDATA[SpeedSeq]]></title>
	<description><![CDATA[<p>A flexible framework for rapid genome analysis and interpretation</p>
<p>C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth (2015). doi:10.1038/nmeth.3505.</p>
<p><a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html">http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html</a></p><p>Address of the bookmark: <a href="https://github.com/hall-lab/speedseq" rel="nofollow">https://github.com/hall-lab/speedseq</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/31568/pacbio-long-reads-compatible-software-and-tools</guid>
	<pubDate>Wed, 15 Mar 2017 14:19:01 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/31568/pacbio-long-reads-compatible-software-and-tools</link>
	<title><![CDATA[Pacbio Long Reads Compatible Software and Tools]]></title>
	<description><![CDATA[<p>The following software packages are known to be compatible with PacBio&reg; data, in addition to PacBio's own SMRT&reg; Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual project sites for up-to-date license information. A separate page lists&nbsp;<a href="http://pacb.com/community/partner_program/current_partners/">commercial software</a>.</p>
<p>Know of any other open source software for PacBio data?&nbsp;<a href="mailto:devnet@pacificbiosciences.com">Email us</a>.</p>
<p>Software categories:</p>
<ul>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#denovo">De novo assembly</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#svdetection">Structural Variations Detection</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#aligners">Reference-based alignment</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#variants">Consensus and variant calling</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#RNA">RNA analysis</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#basemods">Epigenetic base modifications and methylation</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#barcoding">Barcoding</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#browsers">Genome Browsers</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#qc">Run QC</a></li>
<li><a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software#frameworks">Frameworks and APIs</a></li>
</ul><p>Address of the bookmark: <a href="https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software" rel="nofollow">https://github.com/PacificBiosciences/DevNet/wiki/Compatible-Software</a></p>]]></description>
	<dc:creator>Archana Malhotra</dc:creator>
</item>

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