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Graph-based alignment of reads to a population of genomes using hierarchical indexing — successor to TopHat and HISAT for RNA-seq alignment.
Use with AI
Install the MCP server or CLI to instantly fetch HISAT2 documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/hisat2
docker pull biocontainers/hisat2:unknownnf-core/fetchngs — Nextflow pipeline for downloading and standardizing sequencing data from public repositories (SRA, ENA, DDBJ, GEO, Synapse). Fetches FASTQ files from accession IDs and generates nf-
3 shared topics • 2 shared operations
Java command-line tools from the Broad Institute for manipulating high-throughput sequencing data and formats including BAM, CRAM, and VCF.
3 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 • 3 shared operations
PCAWG (Pan-Cancer Analysis of Whole Genomes) pipelines — standardized bioinformatics workflows from the ICGC-TCGA Pan-Cancer consortium for whole-genome somatic analysis of cancer samples. Includes al
2 shared topics • 3 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
3 shared topics • 1 shared operation