SvABA: Structural variation and indel detection by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local...erence with BWA-MEM and parsed to identify variants. Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read supp...1521 days ago
1503 days ago
GRIDSS: the Genomic Rearrangement IDentification Software Suite
GRIDSS is a module software suite containing tools useful for the detection of geno...ll as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided pos...1453 days ago
1441 days ago
SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator
SVEngine (Structural Variants Engine) SVEngine is a multi-purpose and self-contained simulator for...s in cancer. SVEngine outpus alterred contigs in FASTA files, spiked-in variants in VAR files (see Manual), si...1405 days ago
1353 days ago
URMAP, an ultra-fast read mapper
URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA...y 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased agains...1287 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
The DADA2 tutorial goes through a typical workflow for paired end Illumin...on sequencing data is processed into the table of exact amplicon sequence variants (ASVs) present in each s...1275 days ago
maftools : Summarize, Analyze and Visualize MAF Files
With advances in Cancer Genomics, Mutation Annotat...is being widely accepted and used to store somatic variants detected. The Cancer Gen...00. Resulting data consisting of somatic variants are stored in the form of&nbs...1233 days ago
FiNGS: Filters for Next Generation Sequencing
Key features Filters SNVs from any variant caller to remove false positives Cal...tions FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy...1167 days ago