gsnap.nosimd

spliced and SNP-tolerant alignment for mRNA and short reads

Install

All systems
curl cmd.cat/gsnap.nosimd.sh
Ubuntu
apt-get install gmap
image/svg+xml Kali Linux
apt-get install gmap
Windows (WSL2)
sudo apt-get update sudo apt-get install gmap
Dockerfile
dockerfile.run/gsnap.nosimd

gmap

spliced and SNP-tolerant alignment for mRNA and short reads

This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of * known splice sites and identify novel splice sites. * known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA.