2599 days ago
Computational Genomics: Applied Comparative Genomics
...tions, but the techniques will be broadly applicable across the tree of life. The topics will include genome assembly & comparative genomics, variant identification & analysis...2356 days ago
Harvest: a suite of core-genome alignment and visualization tools
...ckly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detectio...lysis Gingr - Interactive visualization of alignments, trees and variants HarvestTools - Archivi...2347 days ago
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
...IRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing da...reference material showed up to ∼98% reduction of false variants when combined to conventiona...2333 days ago
2172 days ago
Ranbow: a haplotype assembler for polyploid genomes
...Ranbow can also be applied to other polyploid genomes. After a first phasing, Ranbow utilizes the assembled haplotypes to improve the accuracy of variant calling results and to infer...2172 days ago
gSearch: a fast and flexible general search tool for whole-genome sequencing
gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner.2105 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
...er, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and...eted short read sequencing data, integrates well with standard somatic variant detection and copy number pip...2103 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
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...2032 days ago
Ensembl Variation - Calculated variant consequences
For each variant that is mapped to the reference genome, we identi...ch to predict the effects that each allele of the variant may have on each transcript....in the table below. Note that each allele of each variant may have a different effect i...2071 days ago