Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

Investigators: Gerton Lunter and Martin Goodson
Description: Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features:
  • Maps single, paired-end and mate pair Illumina reads to a reference genome
  • Fast: about 20 Gbase per hour in hybrid mode (using BWA)
  • Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome
  • High sensitivity for indels and divergent reads, up to 10-15%
  • Low mapping bias for reads with SNPs
  • Well calibrated mapping quality scores
  • Input: Fastq and Fasta; gzipped or plain
  • Output: SAM, Maq's map file
  • Optionally calculates per-base alignment posteriors
  • Optionally processes part of the input
  • Handles reads of up to 4500 bases
Reference: Lunter and Goodson. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2011. 21:936-939. (Link to paper)

Stampy documentation
Stampy registration and download

Contact: Gerton Lunter