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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/37561?offset=100</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34528/cope-an-accurate-k-mer-based-pair-end-reads-connection-tool-to-facilitate-genome-assembly</guid>
	<pubDate>Wed, 06 Dec 2017 02:08:14 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34528/cope-an-accurate-k-mer-based-pair-end-reads-connection-tool-to-facilitate-genome-assembly</link>
	<title><![CDATA[COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly]]></title>
	<description><![CDATA[<p><span>An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30&times; simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE connected over 99% of reads with 98.8% accuracy, which is, respectively, 10 and 2% higher than the recently published tool FLASH. When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer errors and give a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected reads.</span></p><p>Address of the bookmark: <a href="ftp://ftp.genomics.org.cn/pub/cope" rel="nofollow">ftp://ftp.genomics.org.cn/pub/cope</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</guid>
	<pubDate>Tue, 08 May 2018 04:27:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads</link>
	<title><![CDATA[HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads]]></title>
	<description><![CDATA[<p><strong>HISAT2</strong><span>&nbsp;is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs&nbsp;</span><a href="http://dl.acm.org/citation.cfm?id=2674828">[Sir&eacute;n et al. 2014]</a><span>, we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).&nbsp;</span></p>
<p><span>more at&nbsp;https://ccb.jhu.edu/software/hisat2/index.shtml</span></p><p>Address of the bookmark: <a href="https://github.com/infphilo/hisat2" rel="nofollow">https://github.com/infphilo/hisat2</a></p>]]></description>
	<dc:creator>Rahul Nayak</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/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share</guid>
	<pubDate>Tue, 07 Aug 2018 04:41:07 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37502/alignqc-a-tool-for-assessing-an-alignment-and-generating-reports-that-are-easy-to-share</link>
	<title><![CDATA[AlignQC: A tool for assessing an alignment, and generating reports that are easy to share]]></title>
	<description><![CDATA[<p><span>Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.</span></p>
<p>https://f1000research.com/articles/6-100/</p>
<p>https://github.com/jason-weirather/AlignQC</p><p>Address of the bookmark: <a href="https://www.healthcare.uiowa.edu/labs/au/AlignQC/" rel="nofollow">https://www.healthcare.uiowa.edu/labs/au/AlignQC/</a></p>]]></description>
	<dc:creator>Jit</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/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/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/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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