Loading homepage
nf-core/chipseq — Nextflow pipeline for comprehensive ChIP-seq analysis from raw reads through peak calling and differential analysis. Automates adapter trimming, multi-aligner support (BWA, Bowtie2,
Use with AI
Install the MCP server or CLI to instantly fetch nf-corechipseq documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/nf-corechipseq
Fastq Screen — Perl tool for screening FASTQ sequencing reads against multiple reference genomes to detect sample contamination. Maps reads to user-defined genome databases (human, mouse, E. coli, Phi
2 shared topics • 2 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
KneadData — quality control and host decontamination tool for metagenomic
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