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.

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  1. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)