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AfterQC — automatic filtering, trimming, error removing and quality control for FASTQ data. Processes Illumina paired-end and single-end reads with automatic adapter detection, overlap-based error cor

2 shared topics • 2 shared operations

HiCUP (Hi-C User Pipeline) is a modular pipeline for mapping and performing quality control on Hi-C sequencing data. Processes paired-end FASTQ reads through four stages: truncation at ligation juncti

2 shared topics • 2 shared operations

PLINK/SEQ — open-source C/C++ library and command-line tool (pseq) for working with human genetic variation data from large-scale resequencing projects. Use when working with VCF loading, variant filt

2 shared topics • 2 shared operations

VCFtools — C++ toolkit for filtering, comparing, summarizing, converting, and manipulating VCF (Variant Call Format) and BCF files. Provides site and individual-level filtering, allele frequency calcu

2 shared topics • 2 shared operations

AGAT (Another Gff Analysis Toolkit) — comprehensive Perl toolkit for reading, writing, validating, fixing, and manipulating genome annotation files in GFF3, GTF, and GFF2 formats. Converts between for

1 shared topic • 3 shared operations