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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/38634?offset=50</link>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44219/chromosome-breakpoint-a-breakup-to-remember</guid>
	<pubDate>Tue, 07 Mar 2023 13:31:54 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44219/chromosome-breakpoint-a-breakup-to-remember</link>
	<title><![CDATA[Chromosome breakpoint - a breakup to remember]]></title>
	<description><![CDATA[<div><div><div><div><div><div><div><div><div><div><p>Chromosome breakpoint refers to the physical location where a chromosome is broken and rearranged. Chromosome breakage can occur spontaneously or be induced by environmental factors such as radiation, chemicals, or viruses. The rearrangement of genetic material resulting from a chromosome breakpoint can have important consequences, including the development of genetic diseases, chromosomal abnormalities, or cancer.</p><p>Chromosome breakpoints can occur in two ways: interstitial or terminal. Interstitial breakpoints occur within the chromosome, while terminal breakpoints occur at the end of the chromosome. Terminal breakpoints can lead to the loss of genetic material, whereas interstitial breakpoints can result in the duplication or deletion of genetic material.</p><p>Chromosome breakpoints can be detected using a variety of techniques, including cytogenetic analysis, fluorescence in situ hybridization (FISH), and molecular methods such as polymerase chain reaction (PCR) and next-generation sequencing (NGS). These techniques can also help identify the exact location of the breakpoint and the nature of the rearrangement, such as translocations, inversions, deletions, or duplications.</p><p>Translocations are one of the most common types of chromosome rearrangements caused by breakpoints. In a translocation, genetic material is exchanged between two different chromosomes, resulting in a balanced or unbalanced distribution of genetic material. Unbalanced translocations can cause genetic diseases or developmental abnormalities, while balanced translocations can be inherited without any apparent phenotypic effects.</p><p>Inversions occur when a chromosome segment is inverted, resulting in a change in the order of genetic material. Inversions can be pericentric, involving the centromere, or paracentric, not involving the centromere. Inversions can cause genetic diseases or phenotypic effects if they disrupt the function of essential genes or regulatory elements.</p><p>Deletions and duplications are caused by interstitial breakpoints that result in the loss or gain of genetic material. Deletions can cause genetic diseases or developmental abnormalities if they involve essential genes or regulatory elements. Duplications can also have phenotypic effects, depending on the location and size of the duplicated segment.</p><p>Chromosome breakpoints can also be involved in the formation of complex chromosomal rearrangements, such as ring chromosomes or dicentric chromosomes. These complex rearrangements can have important clinical implications, as they can cause genetic diseases or cancer.</p><p>In conclusion, chromosome breakpoints are important genetic events that can lead to the rearrangement of genetic material and have important clinical implications. The detection and characterization of chromosome breakpoints using cytogenetic, molecular, and genomic methods are essential for the diagnosis, prognosis, and treatment of genetic diseases and cancer. Further research is needed to understand the molecular mechanisms underlying chromosome breakage and to develop new therapies targeting these events.</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/34292/automatic-filtering-trimming-error-removing-and-quality-control-for-fastq-data</guid>
	<pubDate>Mon, 13 Nov 2017 05:10:23 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34292/automatic-filtering-trimming-error-removing-and-quality-control-for-fastq-data</link>
	<title><![CDATA[Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data]]></title>
	<description><![CDATA[<p><span>Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data</span><br><code>AfterQC</code><span>&nbsp;can simply go through all fastq files in a folder and then output three folders:&nbsp;</span><span>good</span><span>,&nbsp;</span><span>bad</span><span>&nbsp;and&nbsp;</span><span>QC</span><span>&nbsp;folders, which contains good reads, bad reads and the QC results of each fastq file/pair.</span><br><span>Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other&nbsp;</span><a href="http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_FASTQFiles.htm">Illumina 1.8 or newer formats</a></p><p>Address of the bookmark: <a href="https://github.com/OpenGene/AfterQC" rel="nofollow">https://github.com/OpenGene/AfterQC</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/34504/minion-gc-an-r-script-to-do-some-qc-on-minion-data</guid>
	<pubDate>Sun, 03 Dec 2017 15:19:18 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/34504/minion-gc-an-r-script-to-do-some-qc-on-minion-data</link>
	<title><![CDATA[MinION_GC: An R script to do some QC on MinION data]]></title>
	<description><![CDATA[<p><span>Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single, small, .txt summary file. So it's a lot quicker than most other things out there: it takes about a minute to analyse a 4GB flowcell on my laptop.</span></p>
<p>https://github.com/roblanf/minion_qc</p><p>Address of the bookmark: <a href="https://github.com/roblanf/minion_qc" rel="nofollow">https://github.com/roblanf/minion_qc</a></p>]]></description>
	<dc:creator>Radha Agarkar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/36518/mix-combining-multiple-assemblies-from-ngs-data</guid>
	<pubDate>Tue, 08 May 2018 04:58:05 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/36518/mix-combining-multiple-assemblies-from-ngs-data</link>
	<title><![CDATA[MIX: Combining multiple assemblies from NGS data]]></title>
	<description><![CDATA[<p>Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.</p>
<p>The Mix algorithm, approach and results were published in BMC bioinformatics :&nbsp;<a href="http://www.biomedcentral.com/1471-2105/14/S15/S16">http://www.biomedcentral.com/1471-2105/14/S15/S16</a>.</p><p>Address of the bookmark: <a href="https://github.com/cbib/MIX" rel="nofollow">https://github.com/cbib/MIX</a></p>]]></description>
	<dc:creator>Rahul Nayak</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/37498/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data</guid>
	<pubDate>Mon, 06 Aug 2018 17:24:53 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/37498/nextsv-a-meta-caller-for-structural-variants-from-low-coverage-long-read-sequencing-data</link>
	<title><![CDATA[NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data]]></title>
	<description><![CDATA[<p>NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different analysis purpose. The output of NextSV is in ANNOVAR-compatible bed format. Users can easily perform downstream annotation using ANNOVAR and disease gene discovery using Phenolyzer.</p>
<p>&nbsp;</p>
<h2>&nbsp;</h2><p>Address of the bookmark: <a href="https://github.com/Nextomics/NextSV" rel="nofollow">https://github.com/Nextomics/NextSV</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38172/bamview-a-free-interactive-display-of-read-alignments-in-bam-data-files</guid>
	<pubDate>Fri, 09 Nov 2018 13:43:22 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38172/bamview-a-free-interactive-display-of-read-alignments-in-bam-data-files</link>
	<title><![CDATA[BamView: a free interactive display of read alignments in BAM data files]]></title>
	<description><![CDATA[<p>To run the application on UNIX from the downloaded jar file run the UNIX:</p>
<p><tt>java -mx512m -jar BamView.jar</tt></p>
<p>and extra command line options are given when '-h' is used:</p>
<p><tt>java -jar BamView.jar -h</tt></p>
<p>BAM files can be specified on the command line with the '-a' option:</p>
<p><tt>java -mx512m -jar BamView.jar -a pathToFile/sorted.bam</tt></p>
<p>If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="http://bamview.sourceforge.net/" rel="nofollow">http://bamview.sourceforge.net/</a></p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/38598/zenbu-a-collaborative-omics-data-integration-and-interactive-visualization-system</guid>
	<pubDate>Fri, 04 Jan 2019 13:35:26 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/38598/zenbu-a-collaborative-omics-data-integration-and-interactive-visualization-system</link>
	<title><![CDATA[ZENBU: a collaborative, omics data integration and interactive visualization system]]></title>
	<description><![CDATA[<p><span>ZENBU</span><span>&nbsp;</span><span>is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for novel data exploration through "on-demand" data processing and interactive linked-visualizations and is able to make many-views from the same primary sequence alignment data which users can uploaded from BAM, BED, GFF and tab-text files.&nbsp;<br>Please check our&nbsp;<a href="http://fantom.gsc.riken.jp/zenbu/wiki">documentation wiki</a>&nbsp;for details on how to use the system, or check out some of the views above.</span></p><p>Address of the bookmark: <a href="http://fantom.gsc.riken.jp/zenbu/" rel="nofollow">http://fantom.gsc.riken.jp/zenbu/</a></p>]]></description>
	<dc:creator>BioJoker</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data</guid>
	<pubDate>Sat, 25 Jan 2020 13:28:09 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/40611/deepvariant-an-analysis-pipeline-that-uses-a-deep-neural-network-to-call-genetic-variants-from-next-generation-dna-sequencing-data</link>
	<title><![CDATA[DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.]]></title>
	<description><![CDATA[<p><span>DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.</span></p>
<p><span><span>DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant relies on&nbsp;</span><a href="https://github.com/google/nucleus">Nucleus</a><span>, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the&nbsp;</span><a href="https://www.tensorflow.org/">TensorFlow</a><span>&nbsp;machine learning framework.</span></span></p>
<p><span><a href="https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html">https://ai.googleblog.com/2017/12/deepvariant-highly-accurate-genomes.html</a></span></p>
<p><span><a href="https://www.biorxiv.org/content/10.1101/092890v6">https://www.biorxiv.org/content/10.1101/092890v6</a></span></p>
<p><span><img src="https://4.bp.blogspot.com/-2KlXZO60sWE/WiGc8qlZfxI/AAAAAAAACOs/s1pNiKI8jsAvJLr1E_po5udDO8eObm_awCLcBGAs/s640/image3.png" width="640" height="427" alt="image" style="border: 0px;"></span></p><p>Address of the bookmark: <a href="https://github.com/google/deepvariant" rel="nofollow">https://github.com/google/deepvariant</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats</guid>
	<pubDate>Tue, 18 Feb 2020 03:36:22 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41148/pbmm2a-minimap2-frontend-for-pacbio-native-data-formats</link>
	<title><![CDATA[pbmm2:A minimap2 frontend for PacBio native data formats]]></title>
	<description><![CDATA[<p><em>pbmm2</em> is a SMRT C++ wrapper for <a href="https://github.com/lh3/minimap2">minimap2</a>'s C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to <em>pbmm2</em>. Benchmarks show that <em>pbmm2</em> outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. <em>pbmm2</em> is the official replacement for BLASR.</p><p>Address of the bookmark: <a href="https://github.com/PacificBiosciences/pbmm2" rel="nofollow">https://github.com/PacificBiosciences/pbmm2</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/41730/parliament2-runs-a-combination-of-tools-to-generate-structural-variant-calls-on-whole-genome-sequencing-data</guid>
	<pubDate>Thu, 28 May 2020 21:57:03 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/41730/parliament2-runs-a-combination-of-tools-to-generate-structural-variant-calls-on-whole-genome-sequencing-data</link>
	<title><![CDATA[Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome sequencing data]]></title>
	<description><![CDATA[<p>Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations between two regions in the genome.</p>
<p>Parliament2 runs a combination of tools to generate structural variant calls on whole-genome sequencing data. It can run the following callers: Breakdancer, Breakseq2, CNVnator, Delly2, Manta, and Lumpy. Because of synergies in how the programs use computational resources, these are all run in parallel. Parliament2 will produce the outputs of each of the tools for subsequent investigation.</p><p>Address of the bookmark: <a href="https://github.com/dnanexus/parliament2" rel="nofollow">https://github.com/dnanexus/parliament2</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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