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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/37962?offset=180</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34445/inc-seq-accurate-single-molecule-reads-using-nanopore-sequencing</guid>
	<pubDate>Mon, 27 Nov 2017 10:38:56 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34445/inc-seq-accurate-single-molecule-reads-using-nanopore-sequencing</link>
	<title><![CDATA[INC-Seq: accurate single molecule reads using nanopore sequencing]]></title>
	<description><![CDATA[<p><span>INC-Seq reads enabled accurate species-level classification, identification of species at 0.1&nbsp;% abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.</span></p><p>Address of the bookmark: <a href="https://github.com/CSB5/INC-Seq" rel="nofollow">https://github.com/CSB5/INC-Seq</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</guid>
	<pubDate>Mon, 30 Apr 2018 04:38:40 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36456/alpaca-a-hybrid-strategy-for-assembly-of-genomic-dna-shotgun-sequencing-reads</link>
	<title><![CDATA[ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.]]></title>
	<description><![CDATA[<p><span>ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set.&nbsp;</span></p>
<p><span>Detail paper at&nbsp;https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-8</span></p><p>Address of the bookmark: <a href="https://github.com/VicugnaPacos/ALPACA" rel="nofollow">https://github.com/VicugnaPacos/ALPACA</a></p>]]></description>
	<dc:creator>Seema Singh</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36635/circlator-automated-circularization-of-genome-assemblies-using-long-sequencing-reads</guid>
	<pubDate>Tue, 15 May 2018 09:42:32 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36635/circlator-automated-circularization-of-genome-assemblies-using-long-sequencing-reads</link>
	<title><![CDATA[Circlator: automated circularization of genome assemblies using long sequencing reads]]></title>
	<description><![CDATA[A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. 

Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 10.1186/s13059-015-0849-0. PMID: 26714481.<p>Address of the bookmark: <a href="http://sanger-pathogens.github.io/circlator/" rel="nofollow">http://sanger-pathogens.github.io/circlator/</a></p>]]></description>
	<dc:creator>Poonam Mahapatra</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36918/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads</guid>
	<pubDate>Tue, 12 Jun 2018 08:14:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36918/p-rna-scaffolder-a-fast-and-accurate-genome-scaffolder-using-paired-end-rna-sequencing-reads</link>
	<title><![CDATA[P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads]]></title>
	<description><![CDATA[P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures of both protein-coding genes and circular RNAs were almost completely recovered and equivalent to those in a complete genome, especially for long proteins and long circular RNAs.<p>Address of the bookmark: <a href="http://www.fishbrowser.org/software/P_RNA_scaffolder/" rel="nofollow">http://www.fishbrowser.org/software/P_RNA_scaffolder/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37574/simlord-a-read-simulator-for-third-generation-sequencing-reads</guid>
	<pubDate>Wed, 22 Aug 2018 10:40:27 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37574/simlord-a-read-simulator-for-third-generation-sequencing-reads</link>
	<title><![CDATA[SimLoRD: A read simulator for third generation sequencing reads]]></title>
	<description><![CDATA[<p>SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model.</p>
<p>Reads are simulated from both strands of a provided or randomly generated reference sequence.</p>
<div id="rst-header-features">
<ul>
<li>The reference can be read from a FASTA file or randomly generated with a given GC content. It can consist of several chromosomes, whose structure is respected when drawing reads. (Simulation of genome rearrangements may be incorporated at a later stage.)</li>
<li>The read lengths can be determined in four ways: drawing from a log-normal distribution (typical for genomic DNA), sampling from an existing FASTQ file (typical for RNA), sampling from a a text file with integers (RNA), or using a fixed length</li>
<li>Quality values and number of passes depend on fragment length.</li>
<li>Provided subread error probabilities are modified according to number of passes</li>
<li>Outputs reads in FASTQ format and alignments in SAM format</li>
</ul>
</div><p>Address of the bookmark: <a href="https://bitbucket.org/genomeinformatics/simlord/" rel="nofollow">https://bitbucket.org/genomeinformatics/simlord/</a></p>]]></description>
	<dc:creator>Aaryan Lokwani</dc:creator>
</item>
<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/40946/free-genomics-data</guid>
	<pubDate>Fri, 07 Feb 2020 14:08:31 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40946/free-genomics-data</link>
	<title><![CDATA[Free Genomics data !]]></title>
	<description><![CDATA[<p><span>The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane McCarthy) and colleagues in Pacific Biosciences (Jonas Korlach).</span></p>
<p><a href="https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/">https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/</a></p><p>Address of the bookmark: <a href="https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/" rel="nofollow">https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</guid>
	<pubDate>Mon, 17 Aug 2020 05:21:09 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/42130/shaman-a-user-friendly-website-for-metataxonomic-analysis-from-raw-reads-to-statistical-analysis</link>
	<title><![CDATA[SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis]]></title>
	<description><![CDATA[<p><span>SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, &hellip;).</span><br><span>The bioinformatics treatment is based on Vsearch [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/27781170">Rognes 2016</a><span>] which showed to be both accurate and fast [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/26664811">Wescott 2015</a><span>].The statistical analysis is based on DESeq2 R package [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/20979621">Anders and Huber 2010</a><span>] which robustly identifies the differential abundant features as suggested in [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3974642/">McMurdie and Holmes 2014</a><span>] and [</span><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727335/">Jonsson2016</a><span>]. SHAMAN robustly identifies the differential abundant genera with the Generalized Linear Model implemented in DESeq2 [</span><a href="http://www.ncbi.nlm.nih.gov/pubmed/25516281">Love 2014</a><span>].</span><br><span>SHAMAN is compatible with standard formats for metagenomic analysis (.csv, .tsv, .biom) and figures can be downloaded in several formats. A presentation about SHAMAN is available&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_presentation.pdf">here</a><span>&nbsp;and a poster&nbsp;</span><a href="https://github.com/aghozlane/shaman/blob/master/www/shaman_poster.pdf">here</a><span>.&nbsp;</span></p>
<p><span>More at&nbsp;<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03666-4</a></span></p><p>Address of the bookmark: <a href="https://github.com/aghozlane/shaman" rel="nofollow">https://github.com/aghozlane/shaman</a></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/26975/trimmomatic-a-flexible-read-trimming-tool-for-illumina-ngs-data</guid>
	<pubDate>Fri, 15 Apr 2016 05:58:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/26975/trimmomatic-a-flexible-read-trimming-tool-for-illumina-ngs-data</link>
	<title><![CDATA[Trimmomatic: A flexible read trimming tool for Illumina NGS data]]></title>
	<description><![CDATA[<h4>Paired End:</h4>
<p><code>java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36</code></p>
<p>This will perform the following:</p>
<ul>
<li>Remove adapters (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10)</li>
<li>Remove leading low quality or N bases (below quality 3) (LEADING:3)</li>
<li>Remove trailing low quality or N bases (below quality 3) (TRAILING:3)</li>
<li>Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)</li>
<li>Drop reads below the 36 bases long (MINLEN:36)</li>
</ul>
<p>More at http://www.usadellab.org/cms/?page=trimmomatic</p><p>Address of the bookmark: <a href="http://www.usadellab.org/cms/?page=trimmomatic" rel="nofollow">http://www.usadellab.org/cms/?page=trimmomatic</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>

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