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BWA-MEM2 — accelerated Burrows-Wheeler Aligner for mapping short DNA reads to reference genomes. Use when aligning Illumina WGS, WES, targeted panel, ChIP-seq, or ATAC-seq FASTQ reads. Drop-in replace
Use with AI
Install the MCP server or CLI to instantly fetch BWA-MEM2 documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/bwa-mem2
AlleleSeq — pipeline for detecting allele-specific expression (ASE) and allele-specific binding (ASB) from RNA-seq and ChIP-seq data at heterozygous SNP positions. Constructs a personal diploid genome
2 shared topics • 2 shared operations
BaalChIP — Bioconductor R package for detecting allele-specific binding (ASB) in ChIP-seq data. Identifies allelic imbalance at heterozygous SNPs using a Bayesian statistical framework with logistic r
2 shared topics • 2 shared operations
BPNet — deep learning framework for learning base-resolution regulatory sequence features from genomics assays (ChIP-seq, ATAC-seq, CUT&RUN). Uses dilated convolutional neural networks to predict TF b
2 shared topics • 2 shared operations
WASP (Weight And SNP-based Pipeline) corrects allele-specific mapping bias in RNA-seq and ChIP-seq by SNP-masking reads that overlap heterozygous variants, remapping them, and filtering those that shi
2 shared topics • 2 shared operations
Use when working with vg — the variation graph toolkit — for pangenome graph construction, read mapping to variation graphs, and graph-aware variant calling. Builds genome graphs from VCF + reference
1 shared topic • 3 shared operations