Genome Mapping Made Simple

  • Maps single, paired-end fastq files and mate pair reads to a reference genome
    • Compatible with the following genetic data formats: .fastq, .fastq.gz, .fq and .fq.gz
    • fastq files must be paired reads
  • 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
  • Calculates per-base alignment posteriors (optional)
  • Processes part of the input (optional)

Short Read Mapper generates a large SAM file that will be stored in your account. You can then download the file, share it and use it with other apps in the App Market.

EvE Premium can then be used to convert the SAM into BAM, genome vcf (gVCF), regular VCF and 23andMe txt file

$249 per file

Inputs (Compatible DNA Data Formats)

    • gzipped or plain


  • SAM
    • After this app generates a SAM file, you can further process the SAM file to BAM, genome VCF, regular VCF or 23andMe txt format using EvE Premium.

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