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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/40516?offset=270</link>
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	<description><![CDATA[]]></description>
	
	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37959/rainbow-an-integrated-tool-for-efficient-clustering-and-assembling-rad-seq-reads</guid>
	<pubDate>Fri, 19 Oct 2018 08:23:42 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37959/rainbow-an-integrated-tool-for-efficient-clustering-and-assembling-rad-seq-reads</link>
	<title><![CDATA[Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads]]></title>
	<description><![CDATA[<p><span>Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads using a spaced seed method. Then, Rainbow implements a heterozygote calling like strategy to divide potential groups into haplotypes in a top&ndash;down manner. And along a guided tree, it iteratively merges sibling leaves in a bottom&ndash;up manner if they are similar enough. Here, the similarity is defined by comparing the 2nd reads of a RAD segment. This approach tries to collapse heterozygote while discriminate repetitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on simulation and a real guppy RAD-seq data, we show that Rainbow is more competent than the other tools in dealing with RAD-seq data</span></p><p>Address of the bookmark: <a href="https://sourceforge.net/projects/bio-rainbow/files/" rel="nofollow">https://sourceforge.net/projects/bio-rainbow/files/</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<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>
<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/42485/fastprongs-fast-preprocessing-of-next-generation-sequencing-reads</guid>
	<pubDate>Sat, 26 Dec 2020 08:35:21 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42485/fastprongs-fast-preprocessing-of-next-generation-sequencing-reads</link>
	<title><![CDATA[FastProNGS: fast preprocessing of next-generation sequencing reads]]></title>
	<description><![CDATA[<p><span>FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest.&nbsp;</span></p><p>Address of the bookmark: <a href="https://github.com/Megagenomics/FastProNGS" rel="nofollow">https://github.com/Megagenomics/FastProNGS</a></p>]]></description>
	<dc:creator>Rahul Nayak</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/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/40893/quorum-an-error-corrector-for-illumina-reads</guid>
	<pubDate>Tue, 04 Feb 2020 23:26:55 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40893/quorum-an-error-corrector-for-illumina-reads</link>
	<title><![CDATA[QuorUM: An Error Corrector for Illumina Reads]]></title>
	<description><![CDATA[<p><span>We produce trimmed and error-corrected reads that result in assemblies with longer contigs and fewer errors. We compared QuorUM against several published error correctors and found that it is the best performer in most metrics we use. QuorUM is efficiently implemented making use of current multi-core computing architectures and it is suitable for large data sets (1 billion bases checked and corrected per day per core)</span></p><p>Address of the bookmark: <a href="http://www.genome.umd.edu/" rel="nofollow">http://www.genome.umd.edu/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

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