Short Read Mapper |
4.4 3721

Short Read Mapper

Genome mapping made simple

  • Maps single, paired-end and mate pair reads to a reference genome
  • Handles reads of up to 4500 bases
  • Fast: about 20 Gbase per hour
  • High sensitivity for indels and divergent reads, up to 10-15%
  • Low mapping bias for reads with SNPs
  • Well-calibrated mapping quality scores
  • Optionally calculates per-base alignment posteriors
  • Optionally processes part of the input

$19 to process up to four files

  • All four uses of this app must be used within 30 days of purchase.


    • gzipped or plain


  • SAM
    • After this app generates a SAM file, you can further process that SAM file using the Eve app (alignment, variant calling/discovery, annotations and format conversions).

Lunter and Goodson. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2011. 21:936-939.