Results for "variant calling"
Users
About me: ...using next-generation sequencing technologies like shotgun sequencing, linked reads, and long-read sequencing for whole-genome resequencing, variant calling, and transcriptome assembly,...Skills: Variant Calling1133 days ago
Blogs
Bioinformatics PhDs - Cover Letter
OverviewThe reception your cover letter will receive is mo...their third book has been published and Yale comes calling. They often don't seem...and, perhaps more to the point, Yale rarely "comes calling." An even greater burde...3359 days ago
Calling narrow and broad peaks from ChIP-Seq data
Know about the state-of-the-art algorithms implemented in Strand NGS for detecting the...ification (broad peaks) from ChIP-Seq data.Read the benchmarking study on Calling narrow and broad peaks from C...3190 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 that i...1139 days ago
Next Generation Sequencing (NGS) Tutorials
...a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequenc...aining-activities-schedule/archive-2013.html Variant Detection (Model organism) Ad...1CuKkKylVDb03tnN7RSWl5EUzleetn0ctjmvaidPKLxM Variant Detection Introductory tutori...3480 days ago
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Files
Bioinformatics approach to Boar Taint
...onable to many consumers. Detected functional variant(s) underlying boar taint comp...y using Bowtie2. Alignment file then used for calling SNPs and InDels inside previo...SSC5,13, and 7 with the aid of FreeBayes , a variant caller tool. A final list of...3782 days ago
Discussion topics
- Like in case of plant genomes where nature of genome is too complex and huge in size to accomplish complete de novo assembly by current sequencing technology. What would be alternate solution? Can we live in reference free world?
3937 days ago
Pages
Genome Assembly Tools and Software - PART2 !!
The genome assemblers generally take a file of short sequence reads...ds in a SAM file and a set of variant calls in VCF format, HAPCOMPA...Genome Shotgun Assembler and Variant CallerDISCOVAR is a whol...ion and Assembly of Insertion VariantsMindTheGap is a software...2678 days ago
Awesome perl frameworks, libraries and software - PART 2
licheng/gccfilter - gccfilter is a perl filter to colorize and simplify (or exp...tlayer/softlayer-api-perl-client - A set of Perl libraries that assist in calling the SoftLayer API. singingfi...2487 days ago
Top-level pages
- An algorithm is a computable set of steps to achieve a desired result. We use algorithm...hem.The binary search algorithm is an example of a variant of divide and conquer called...bly by using the simplex algorithm. A complex variant...
3939 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...e package] Comparing genomes and assemblies; variant detection Versatile and ope...al, Genome Biol 10(11):R134, 2009 Full Text Calling SNPs without a reference sequ...formatics 26(6):722-9, 2010. Full Text vipR: variant identification in pooled DNA...3772 days ago
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Wire posts
News
- ...or simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an ex...ffected siblings, a pattern that persisted even after excluding common variants.
3539 days ago
Roche has acquired Bina Technologies !!!
...y based 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...3407 days ago
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Opportunity posts
Human Genome Meeting 2014, Geneva, Switzerland
The spectacular advances of the last few years resulted in the rapid analysis of the genome sequence of each individ...faced with the enormous challenges of assigning pathogenicity to each genomic variant...3873 days ago
Research Associate @ INDIAN INSTITUTE OF SPICES RESEARCH
INDIAN INSTITUTE OF SPICES RESEARCH (Indian Council of Agricultural Research) Mariku...m marks prescribed by the Institute in written test only will be eligible for calling for the interview. The number...3763 days ago
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Bio-Scripts
- ...eads in a HiSeqX Illumina Basecalling directory into various catego...sequencing data. CollectVariantCallingMetrics (Picard)...---------------------- Short Variant Discovery:...Tools that perform variant calling and genotyping for short vari...
2068 days ago
- library(vcfR) # Input the files. vcf
2053 days ago
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Tags
Webinar on Fast and Accurate DNA Variant Calling on 26 Apr 2017
Continuing our DNA-Seq webinar series, we'll present Strand NGS v3.0 best-practices: a workflow that identifies highly accurate variants from raw reads. Our best practices workflow is twice as fast as its GATK counterpart, and results in precision/recall rates of up to 99%/98% on whole exome...Tags: webinar, strand ngs, variant calling, dna-seq, bwa-gatk
2564 days ago
- Webinar on Unique Molecular Identifier-powered Ultra-sensitive Variant Calling using Strand NGS - Case Study by Dr. Pandurang Kolekar, Bioinformatics Engineer, Strand Life Sciences Abstract: Unique Molecular Identifiers (UMIs) are short random nucleotide sequences that are increasingly be...
Tags: UMI, Strand NGS, Variant calling, RNA-Seq, small RNA-Seq
2364 days ago
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 where the number of samples is...bsp;option of FreeBayes to generate frequency-based variant calls as well as some other o...1037 days ago
Comment on "List of non-commercial NGS genotype-calling software"
Delly – Structural variant discovery by integrated paired-en...bilistic framework for structural variant discovery. [ paper-2014&...;] manta – Structural variant and indel caller for mapped s...e – structural variant calling and genotyping with existing...1135 days ago
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