Jit
Enthusiast computational biologist with business dream !!!
Our Sponsors
Related items
DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
By Jit 2010 days ago Comments (1)github.com - 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 its accuracy and performance is comparable to existing tools...Ensembl Variation - Calculated variant consequences
By Jit 2929 days agowww.ensembl.org - For each variant that is mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based approach to predict the effects that each allele of the variant may have on each transcript. The set of consequence...Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 2958 days agogithub.com - Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is...AlfaPang: alignment free algorithm for pangenome graph construction
By BioStar 384 days agogithub.com - AlfaPang constructs variation graphs, leveraging its alignment-free and reference-free approach, based solely on intrinsic sequence properties. This design allows AlfaPang's runtime and memory usage to scale linearly with the size of input...AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
By BioStar 3190 days agosourceforge.net - 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...Best Practices for Variant Calling with the GATK
By biogeek 2398 days agowww.broadinstitute.org - The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version...GFAffix : Identifies walk-preserving shared affixes in variation graphs and collapses them into a...
By BioStar 384 days agogithub.com - GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.Calling variants in non-diploid systems
By Neel 1908 days ago Comments (1)training.galaxyproject.org - The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been...Variant Calling Resequencing-Based Genome Inference
By Abhi 777 days agoevomics.org - Variant Calling - Resequencing-Based Genome Inference Erik GarrisonUniversity of Tennessee Health Science CenterWorkshop on Genomics - Český KrumlovJanuary 12,...High Density Sheep SNP Genotyping Chip released!!!
By Rahul Agarwal 4761 days ago"Ovine Infinium® HD SNP BeadChip”, a high definition SNP chip for ship genome
