Sambamba

ballgown -- R/Bioconductor package for flexible isoform-level differential expression analysis of RNA-seq experiments. Works with StringTie output (.ctab files) to test for differential expression at

1 shared topic • 1 shared operation

BAMtools — C++ API and command-line toolkit for reading, writing, sorting, indexing, filtering, merging, splitting, and converting BAM alignment files. Provides JSON-based filter expressions, multi-fo

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RTG Tools — Java-based toolkit from Real Time Genomics for haplotype-aware variant call comparison, VCF filtering, statistics, and pedigree analysis. Primary use: vcfeval for benchmarking variant call

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SeqKit — cross-platform ultrafast toolkit for FASTA/Q file manipulation. 38 subcommands for sequence statistics (stats), filtering by length or quality (seq), pattern searching with mismatches (grep,

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SURVIVOR — C++ toolkit for structural variation (SV) analysis including merging multi-caller VCF files into consensus callsets, SV simulation on reference genomes, benchmarking SV callers against trut

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