Kevler: Reference-free variant discovery in large eukaryotic genomes
Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs), insertion/deletion variants (indels), and structural...Tags: Reference-free, variant, discovery, large, eukaryotic, genomes, snp, ngs
1557 days ago
vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtTags: vt, variant, tool, discovers, short, variants, Next, Generation, Sequencing, data
1557 days ago
Tags: VG, variation, graph, structures, interchange, formats, alignment, genotyping, variant, calling, methods, snp
1557 days ago
LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usua...Tags: LoFreq, sequence, quality, aware, ultra-sensitive, variant, caller, NGS, data
1536 days ago
Tags: Parliament2, structural, variant, calls, whole-genome, sequencing, data, NGS
1435 days ago
truvari: Structural variant comparison tool for VCFs
Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics MotivationTags: truvari, Structural, variant, comparison, tool, VCFs
1402 days ago
Tags: maftools, maf, format, snp, variant, genome, mutation
868 days ago
Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the read alignment and variant caller’s interna...Tags: Merfin, improved, variant, filtering, assembly, evaluation, polishing, k-mer, validation
760 days ago
Minda: a tool for evaluating structural variant (SV) callers
Minda is a tool for evaluating structural variant (SV) callers that standardizes VCF records for compatibility with both germline and somatic SV callers, benchmarks against a single VCF input file, or benchmarks against an ensemble call set created from multiple VCF input files.Tags: Minda, tool, evaluating, structural, variant, SV, callers
33 days ago