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Bowtie2 — ultrafast and memory-efficient short-read aligner using FM-index with gapped alignment and local alignment modes. Standard aligner for ChIP-seq, ATAC-seq, CUT&RUN, CUT&Tag, and general short
Use with AI
Install the MCP server or CLI to instantly fetch Bowtie2 documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/bowtie2
Analyze bioinformatics sample metadata to auto-detect data modality, column semantics, and sequencing platform from CSV/TSV files, SRA RunTables, GEO Series Matrix files, and AnnData .obs exports. Inf
2 shared topics • 1 shared operation
bedGraphToBigWig converts bedGraph coverage files to bigWig binary format for genome browsers (UCSC, IGV, WashU Epigenome Browser). Essential for ChIP-seq, ATAC-seq, RNA-seq, and WGBS coverage tracks.
2 shared topics • 1 shared operation
MACS2/MACS3 — Model-based Analysis of ChIP-Seq for identifying transcription factor binding sites and histone modification enrichment from ChIP-seq, ATAC-seq, and CUT&Tag data. Provides peak calling (
2 shared topics • 1 shared operation
Use when working with phantompeakqualtools — phantompeakqualtools (spp)
2 shared topics • 1 shared operation
Roadmap Epigenomics — NIH Roadmap Epigenomics Mapping Consortium reference epigenomes spanning 111 primary human tissues and cell types. Provides ChIP-seq histone mark tracks (H3K4me1, H3K4me3, H3K27m
2 shared topics • 1 shared operation