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...1410 days ago
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URMAP, an ultra-fast read mapper
...50 reads, URMAP achieves high accuracy (precision 0.998, sensitivity 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased agains...1293 days ago
DADA2: Fast and accurate sample inference from amplicon data with single-nucleotide resolution
...h a typical workflow for paired end Illumina Miseq data: raw amplicon sequencing data is processed into the table of exact amplicon sequence variants (ASVs) present in each s...1281 days ago
maftools : Summarize, Analyze and Visualize MAF Files
...n Format (MAF) is being widely accepted and used to store somatic variants detected. The Cancer Gen...er type being over 200. Resulting data consisting of somatic variants are stored in the form of&nbs...1238 days ago
FiNGS: Filters for Next Generation Sequencing
...eir thresholds) Option to use filters identical to ICGC recommendations FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy...1172 days ago
Calling variants in non-diploid systems
...n-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 t...1053 days ago
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