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 variant...2325 days ago
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Ranbow: a haplotype assembler for polyploid genomes
...ow 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 the evol...2164 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.2097 days ago
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing d...2097 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
...osity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and...g data, integrates well with standard somatic variant detection and copy number pip...orrissey M (2016). “PureCN: Copy number calling and SNV classification using...2095 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...2024 days ago
Ensembl Variation - Calculated variant consequences
For each variant that is mapped to the reference genome, we identify all overlapping Ens...ach 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...2063 days ago
VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To...t to store only those read-pairs or reads who intersect some region around the variant...2038 days ago