Note: These tutorials are incomplete. More complete versions are being made available for our members. Sign up for free.
Hardware Acceleration of Mapping
BWT
Langmead B, Trapnell C, Pop M, Salzberg S (2009) Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome Biol 10: R25.
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores.Genome Res. 18(11):1851-8. Link
SOAP
Lunter G, Goodsib M. (2010) Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads, Genome Research. Link
MUMmer
CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform Bioinformatics (2012) 28(14): 1830-1837
YOABS: yet other aligner of biological sequences–an efficient linearly scaling nucleotide aligner Bioinformatics (2012) 28(8): 1070-1077
H. Li et al. (2009) The Sequence Alignment/Map format and SAMtools
