AfterQC

Hail — scalable Python framework for genomic data analysis built on Apache Spark. Use when performing GWAS, variant quality control, sample QC, PCA, LD pruning, association testing, burden tests, or b

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

PRINSEQ++ — high-performance C++ tool for quality control and preprocessing of FASTQ sequencing reads. Filters and trims reads by quality score, length, GC content, sequence complexity (DUST/entropy),

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