RT Journal
A1 Lunter, Gerton
A1 Goodson, Martin
T1 Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
JF Genome Research 
JO Genome Research 
YR 2011 
FD June 01 
VO 21 
IS 6 
SP 936 
OP 939 
DO 10.1101/gr.111120.110 
UL http://genome.cshlp.org/content/21/6/936.abstract 
AB High-volume sequencing of DNA and RNA is now within reach of any research laboratory and is quickly becoming established as a key research tool. In many workflows, each of the short sequences (“reads”) resulting from a sequencing run are first “mapped” (aligned) to a reference sequence to infer the read from which the genomic location derived, a challenging task because of the high data volumes and often large genomes. Existing read mapping software excel in either speed (e.g., BWA, Bowtie, ELAND) or sensitivity (e.g., Novoalign), but not in both. In addition, performance often deteriorates in the presence of sequence variation, particularly so for short insertions and deletions (indels). Here, we present a read mapper, Stampy, which uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. This results in a higher useable sequence yield and improved accuracy compared to that of existing software.