Results for "INDEL"
Blogs
Computer simulation of genetic mechanism !!
...al isolation by distance models. http://raphael.leblois.free.fr/ indel-Seq-Gen A biological se...nd protein superfamilies http://bioinfolab.unl.edu/~cstrope/isg/ Indelible A powerful and flex...2969 days ago
Software and Tools to detect structure variation with long reads !!
...m/1471-2105/15/180/abstract More at https://sourceforge.net/projects/pb-jelly/ SMRT-SV: Structural variant and indel caller for PacBio reads Structural variant (SV) and indel caller for PacBio reads based...2602 days ago
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Bookmarks
- ...nome and the evidence in the reads. It then attempts to make improvements to the input genome, including: Single base differences Small indels Larger indel or block substitution events...
3003 days ago
- ...t is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate...reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors, but this c...
2867 days ago
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Top-level pages
List of generic simulation software/tools/resource with brief description and homepage !!!
...er general isolation by distance models. http://raphael.leblois.free.fr/indel-Seq-Gen A biological sequence...uences and protein superfamilies http://bioinfolab.unl.edu/~cstrope/isg/Indelible A powerful and flexible s...3731 days ago
Commercial and public next-gen-seq (NGS) software
...s, clean and filter contigs, look for snps and indels., filter snps, do statistics...a fast and memory-efficient manner. Robust to INDELs and MrsFAST has a bisulphite...signed for fast mapping of Illumina reads SNP/Indel Discovery ssahaSNP - ssahaSNP...3513 days ago
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News
- ...and climate change. The recent research provides an unmatched resource to respond to these challenges by identifying a large high-quality SNP and indel data set in diverse sorghum g...
3892 days ago
- ...tools GATK HaplotypeCaller and SOAPindel in test runs on both simulate...al whole human exomes. Like other indel callers, Scalpel works by per...t are a regular source of error in indel calling. When Scalpel assembl...y be linked to a high incidence of indels. One thousand indels from th...
3540 days ago
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Bio-Scripts
- ...E at https://vcftools.github.io/perl_module.html # Calculate stats separately for the filter field, quality and non-indels vcf-stats file.vcf.gz -f FILTER,QUAL=10:200,INFO/INDEL=False -p out/ # Calculat...
1519 days ago
Pack a perl program with their dependencies on Ubuntu !
...orking demo:... Jit@jit.aber SvABA: Structural variation and indel detection by local assemblyBy Jit 6 days ago SvABAStructuralvariationindeldetectionlocalassembly...1505 days ago
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Tags
- Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors...
Tags: Bioinformatics, NGS, Reads, Silulator, INDEL, SNPs, Simulation
2867 days ago
SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window (wi...Tags: SvABA, Structural, variation, indel, detection, local, assembly
1511 days ago
Comments
Comment on "List of non-commercial NGS genotype-calling software"
...sh; lumpy: a general probabilistic framework for structural variant discovery. [ paper-2014 ] manta – Structural variant and indel caller for mapped sequencing...1136 days ago
Comment on "Genome in a Bottle (GIAB) Consortium"
...WS S3 bucket: s3://giab Ongoing and Future work:Current work in the GIAB Analysis Team is focused on establishing benchmark large indel and structural variant calls,...1554 days ago
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