KneadData

nf-core/methylseq — community-curated Nextflow pipeline for whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data analysis. Handles adapter trimming (Tri

2 shared topics • 3 shared operations

IGV (Integrative Genomics Viewer) — high-performance Java desktop application for interactive visualization and exploration of genomic data. Supports BAM/CRAM alignments, VCF variants, BED/GFF annotat

2 shared topics • 2 shared operations

nf-core/atacseq — Nextflow pipeline for ATAC-seq (Assay for Transposase-Accessible Chromatin with sequencing) data analysis. Handles paired- or single-end reads through adapter trimming (Trim Galore),

2 shared topics • 2 shared operations

Qualimap — platform-independent quality control tool for next-generation sequencing alignment data. Provides BAM QC (coverage, insert size, GC content, mapping quality), RNA-seq QC (gene body coverage

2 shared topics • 2 shared operations

vt — C++ command-line variant tool set for manipulating VCF files. Provides variant normalization (left-alignment and trimming), multiallelic decomposition, VCF summary statistics (peek), annotation,

2 shared topics • 2 shared operations