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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/37574?offset=70</link>
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	<description><![CDATA[]]></description>
	
	<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>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41896/kad-assessing-genome-assemblies-using-k-mer-copies-in-assemblies-and-k-mer-abundance-in-illumina-reads</guid>
	<pubDate>Fri, 19 Jun 2020 07:34:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41896/kad-assessing-genome-assemblies-using-k-mer-copies-in-assemblies-and-k-mer-abundance-in-illumina-reads</link>
	<title><![CDATA[KAD: Assessing genome assemblies using K-mer copies in assemblies and K-mer abundance in Illumina reads]]></title>
	<description><![CDATA[<p>KAD is designed for evaluating the accuracy of nucleotide base quality of genome assemblies. Briefly, abundance of k-mers are quantified for both sequencing reads and assembly sequences. Comparison of the two values results in a single value per k-mer, K-mer Abundance Difference (KAD), which indicates how well the assembly matches read data for each k-mer.</p>
<p><a href="https://render.githubusercontent.com/render/math?math=KAD=log_{2}\begin{pmatrix}\frac{c%2Bm}{m(n%2B1)}\end{pmatrix}" target="_blank"><img src="https://render.githubusercontent.com/render/math?math=KAD=log_{2}\begin{pmatrix}\frac{c%2Bm}{m(n%2B1)}\end{pmatrix}" alt="image" style="border: 0px;"></a></p>
<p>where,&nbsp;<em>c</em>&nbsp;is the count of a k-mer from reads,&nbsp;<em>m</em>&nbsp;is the mode of counts of read k-mers, and&nbsp;<em>n</em>&nbsp;is the copy of the k-mer in the assembly.</p><p>Address of the bookmark: <a href="https://github.com/liu3zhenlab/KAD" rel="nofollow">https://github.com/liu3zhenlab/KAD</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/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>
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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>
</item>
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	<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>
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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/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>
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<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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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34216/meraculous-de-novo-genome-assembly-with-short-paired-end-reads</guid>
	<pubDate>Tue, 07 Nov 2017 04:36:10 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34216/meraculous-de-novo-genome-assembly-with-short-paired-end-reads</link>
	<title><![CDATA[Meraculous: De Novo Genome Assembly with Short Paired-End Reads]]></title>
	<description><![CDATA[<p><span>We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast&nbsp;</span><em>Pichia stipitis</em><span>. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the&nbsp;</span><em>k</em><span>-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by &sim;280 bp or &sim;3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed.</span></p><p>Address of the bookmark: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158087/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3158087/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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