DIDA: Distributed Indexing Dispatched Alignment.
One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA), and is free for academic use.
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Bioinformatics, University of British Columbia, Vancouver, BC, Canada; Intel Health and Life Sciences, Intel Corporation, Hillsboro, OR, US.
Hamid
H
Mohamadi
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
Benjamin P
BP
Vandervalk
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada.
Anthony
A
Raymond
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Bioinformatics, University of British Columbia, Vancouver, BC, Canada.
Shaun D
SD
Jackman
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Bioinformatics, University of British Columbia, Vancouver, BC, Canada.
Justin
J
Chu
Intel Health and Life Sciences, Intel Corporation, Hillsboro, OR, US.
Clay P
CP
Breshears
Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.
Inanc
I
Birol
D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D012984:Software