Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

This article is part of the supplement: Selected articles from the Eleventh Asia Pacific Bioinformatics Conference (APBC 2013): Genomics

Open Access Proceedings

Accelerating read mapping with FastHASH

Hongyi Xin1, Donghyuk Lee1, Farhad Hormozdiari2, Samihan Yedkar1, Onur Mutlu1* and Can Alkan3*

Author Affiliations

1 Depts. of Computer Science and Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA

2 Dept. of Computer Science, University of California Los Angeles, Los Angeles, CA, 90095, USA

3 Dept. of Computer Engineering, Bilkent University, Ankara, 06800, Turkey

For all author emails, please log on.

BMC Genomics 2013, 14(Suppl 1):S13  doi:10.1186/1471-2164-14-S1-S13

Published: 21 January 2013

Additional files

Additional file 1:

Performance on Real Data Sets. Performance comparison between different methods, while using three different data sets. Set 1 is a set of 1 million reads of length 160 bp obtained from a human genome sequenced within the 1000 Genomes Project. Set 2 is composed of 500,000 reads of length 101 bp generated from a chimpanzee genome, and Set 3 is from an orangutan genome with reads of length 75 bp (500,000 reads). We select edit distance values from 1 to 5 in order to compare the speed (time), sensitivity (Reads Mapped) and comprehensiveness (Map Locations) of each mapper.

Format: XLSX Size: 49KB Download file

Open Data