Results for "calling"
Users
About me: ...ng next-generation sequencing technologies like shotgun sequencing, linked reads, and long-read sequencing for whole-genome resequencing, variant calling, and transcriptome assembly,...Skills: Variant Calling1131 days ago
Blogs
Bioinformatics PhDs - Cover Letter
...pastures as soon as their third book has been published and Yale comes calling. They often don't seem...l and professional, and, perhaps more to the point, Yale rarely "comes calling." An even greater burde...3357 days ago
Calling narrow and broad peaks from ChIP-Seq data
...scription factor (narrow peaks) and enriched regions of histone modification (broad peaks) from ChIP-Seq data.Read the benchmarking study on Calling narrow and broad peaks from C...3188 days ago
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Bookmarks
DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found th...1137 days ago
Next Generation Sequencing (NGS) Tutorials
...eqFlow: Workflows for RNA-Seq data analysis DOI: 10.1093/bioinformatics/btr441 ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequenc...3478 days ago
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Files
Bioinformatics approach to Boar Taint
...ort reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file then used for calling SNPs and InDels inside previo...3780 days ago
Pages
Awesome perl frameworks, libraries and software - PART 2
...sstrigler/chatbot - a jabber channel bot written in perl softlayer/softlayer-api-perl-client - A set of Perl libraries that assist in calling the SoftLayer API. singingfi...2485 days ago
Top-level pages
Useful Publications and Websites for Deep Sequencing Data Analysis
...e for full-genome alignment & comparisons] Searching for SNPs with cloud computing. Langmead et al, Genome Biol 10(11):R134, 2009 Full Text Calling SNPs without a reference sequ...3770 days ago
Next generation sequencing in R or bioconductor environment
...The chipseq package combines a variety of HT-Seq packages to a pipeline for ChIP-Seq data analysis. Documentation BayesPeak BayesPeak is a peak calling package for identifying DNA b...3615 days ago
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Wire posts
News
- ...y check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an ex...
3537 days ago
Roche has acquired Bina Technologies !!!
...sed in California. The biotech’s first product was the Bina Box, a platform for secondary genomic analysis, sequence alignment, and variant calling, but since 2012, it has devel...3405 days ago
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Opportunity posts
Research Associate @ INDIAN INSTITUTE OF SPICES RESEARCH
...mination Hall after 10.00 A.M. 6. Candidates who secure the minimum marks prescribed by the Institute in written test only will be eligible for calling for the interview. The number...3761 days ago
Research Associate @ INDIAN INSTITUTE OF SPICES RESEARCH
...mination Hall after 10.00 A.M. 6. Candidates who secure the minimum marks prescribed by the Institute in written test only will be eligible for calling for the interview. The number...3775 days ago
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Bio-Scripts
- ...--------------------------- Base Calling:...lidity for specified Illumina basecalling data. CollectIlluminaB...ng reads in a HiSeqX Illumina Basecalling directory into various catego...Tools that perform variant calling and genotyping for short vari...
2066 days ago
Samtools commands for bioinformatician !
...-g -f sal_ref_sej.fasta sal_sej_sorted.bam.bam > sal_vars.bcf ### calling snp and indels # -c : find s...is "call". type "bcftools" to see current version and commands ### calling snp and indels with no freque...1594 days ago
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Tags
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-hou...Tags: AIRVF, filtering, toolbox, precise, variant, calling, Ion, Torrent, sequencing
2317 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number...Tags: PureCN, copy, number, calling, SNV, classification, targeted, short, read, sequencing
2087 days ago
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Comments
Comment on "Calling variants in non-diploid systems"
FreeBayes is widely used for calling variants in diploid systems. However, it can also be used for calling variants in pooled samples wh...1035 days ago
Comment on "List of non-commercial NGS genotype-calling software"
...idss – GRIDSS: the Genomic Rearrangement IDentification Software Suite. [ paper-2017 ]smoove – structural variant calling and genotyping with existing...1133 days ago
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