mrsFAST: a cache-oblivious algorithm for short-read mapping

Faraz Hach; Fereydoun Hormozdiari; Can Alkan; Farhad Hormozdiari; Inanc Birol; Evan E Eichler; S Cenk Sahinalp

doi:10.1038/nmeth0810-576

mrsFAST: a cache-oblivious algorithm for short-read mapping

Nature Methods ◽

10.1038/nmeth0810-576 ◽

2010 ◽

Vol 7 (8) ◽

pp. 576-577 ◽

Cited By ~ 186

Author(s):

Faraz Hach ◽

Fereydoun Hormozdiari ◽

Can Alkan ◽

Farhad Hormozdiari ◽

Inanc Birol ◽

...

Keyword(s):

Read Mapping ◽

Short Read ◽

Short Read Mapping ◽

Cache Oblivious

Download Full-text

SEAL: a distributed short read mapping and duplicate removal tool

Bioinformatics ◽

10.1093/bioinformatics/btr325 ◽

2011 ◽

Vol 27 (15) ◽

pp. 2159-2160 ◽

Cited By ~ 85

Author(s):

L. Pireddu ◽

S. Leo ◽

G. Zanetti

Keyword(s):

Read Mapping ◽

Short Read ◽

Short Read Mapping

Download Full-text

Short Read Mapping: An Algorithmic Tour

Proceedings of the IEEE ◽

10.1109/jproc.2015.2455551 ◽

2017 ◽

Vol 105 (3) ◽

pp. 436-458 ◽

Cited By ~ 30

Author(s):

Stefan Canzar ◽

Steven L. Salzberg

Keyword(s):

Read Mapping ◽

Short Read ◽

Short Read Mapping

Download Full-text

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

2010 13th IEEE International Conference on Computational Science and Engineering ◽

10.1109/cse.2010.29 ◽

2010 ◽

Cited By ~ 13

Author(s):

Ashwin M. Aji ◽

Liqing Zhang ◽

Wu-chun Feng

Keyword(s):

Graphics Processors ◽

Read Mapping ◽

Short Read ◽

Short Read Mapping

Download Full-text

A new approach for approximate text search using genomic short-read mapping model

Proceedings of the 9th International Conference on Ubiquitous Information Management and Communication - IMCOM '15 ◽

10.1145/2701126.2701151 ◽

2015 ◽

Author(s):

Sung-Hwan Kim ◽

Hwan-Gue Cho

Keyword(s):

Text Search ◽

Read Mapping ◽

New Approach ◽

Short Read ◽

Mapping Model ◽

Short Read Mapping

Download Full-text

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

PLoS ONE ◽

10.1371/journal.pone.0090581 ◽

2014 ◽

Vol 9 (3) ◽

pp. e90581 ◽

Cited By ~ 161

Author(s):

Wan-Ping Lee ◽

Michael P. Stromberg ◽

Alistair Ward ◽

Chip Stewart ◽

Erik P. Garrison ◽

...

Keyword(s):

Next Generation Sequencing ◽

Next Generation ◽

Read Mapping ◽

Short Read ◽

Short Read Mapping ◽

Generation Sequencing

Download Full-text

An Efficient GPUAccelerated Implementation of Genomic Short Read Mapping with BWAMEM

ACM SIGARCH Computer Architecture News ◽

10.1145/3039902.3039910 ◽

2017 ◽

Vol 44 (4) ◽

pp. 38-43 ◽

Cited By ~ 3

Author(s):

Ernst Joachim Houtgast ◽

VladMihai Sima ◽

Koen Bertels ◽

Zaid AlArs

Keyword(s):

Read Mapping ◽

Short Read ◽

Short Read Mapping

Download Full-text

Accelerating short read mapping on an FPGA (abstract only)

Proceedings of the ACM/SIGDA international symposium on Field Programmable Gate Arrays - FPGA '12 ◽

10.1145/2145694.2145740 ◽

2012 ◽

Cited By ~ 4

Author(s):

Yupeng Chen ◽

Bertil Schmidt ◽

Douglas Leslie Maskell

Keyword(s):

Read Mapping ◽

Short Read ◽

Short Read Mapping

Download Full-text

Unified View of Backward Backtracking in Short Read Mapping

Algorithms and Applications - Lecture Notes in Computer Science ◽

10.1007/978-3-642-12476-1_13 ◽

2010 ◽

pp. 182-195 ◽

Cited By ~ 6

Author(s):

Veli Mäkinen ◽

Niko Välimäki ◽

Antti Laaksonen ◽

Riku Katainen

Keyword(s):

Read Mapping ◽

Short Read ◽

Short Read Mapping ◽

Unified View

Download Full-text

Hardware acceleration of BWA-MEM genomic short read mapping for longer read lengths

Computational Biology and Chemistry ◽

10.1016/j.compbiolchem.2018.03.024 ◽

2018 ◽

Vol 75 ◽

pp. 54-64 ◽

Cited By ~ 19

Author(s):

Ernst Joachim Houtgast ◽

Vlad-Mihai Sima ◽

Koen Bertels ◽

Zaid Al-Ars

Keyword(s):

Hardware Acceleration ◽

Read Mapping ◽

Short Read ◽

Short Read Mapping

Download Full-text

A variable length hash method for faster short read mapping on FPGA

2015 25th International Conference on Field Programmable Logic and Applications (FPL) ◽

10.1109/fpl.2015.7293938 ◽

2015 ◽

Cited By ~ 1

Author(s):

Yoko Sogabe ◽

Tsutomu Maruyama

Keyword(s):

Variable Length ◽

Read Mapping ◽

Short Read ◽

Short Read Mapping

Download Full-text