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GMAP/GSNAP — splice-aware genomic alignment suite for mRNA, cDNA, EST, and short-read sequences. GMAP maps long cDNA/mRNA/EST sequences to a genome and identifies intron boundaries, alternative splici
Use with AI
Install the MCP server or CLI to instantly fetch GMAP/GSNAP documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/gmapgsnap
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
Use when performing HLA typing from RNA-seq data with arcasHLA. Covers extracting HLA reads from STAR-aligned BAMs, high-resolution genotyping at 6-digit allele level, partial genotyping for low-cover
2 shared topics • 2 shared operations
FLAMES — Full-Length Analysis of Mutations and Splicing for bulk and single-cell long-read RNA-seq data. R/Bioconductor pipeline for barcode demultiplexing, isoform discovery, transcript quantificatio
2 shared topics • 2 shared operations
Loom — HDF5-based file format and Python library (loompy) for storing and accessing large single-cell RNA-seq datasets. Supports sparse/dense matrices, row attributes (genes/features), column attribut
2 shared topics • 2 shared operations
Novocraft suite — short-read alignment and BAM sorting for DNA-seq and RNA-seq. novoalign maps Illumina, Ion Torrent, and 454 reads to indexed reference genomes with Smith-Waterman scoring for high-ac
2 shared topics • 2 shared operations