DIDA

DIDA is a novel framework that performs the large-scale alignment tasks by distributing the indexing and alignment stages into smaller subtasks over a cluster of compute nodes.

Project Description

DIDA

One of the most essential applications in bioinformatics affected by High-Throughput Sequencing (HTS) 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 problem becomes a computationally challenging problem. This is especially true when targets are dynamic such as intermediate steps of a de novo assembly process. To address this problem, we have designed and developed DIDA, a distributed and parallel indexing and alignment algorithm. First, we partition the targets into smaller parts using a heuristic balanced cut. Next, we create an index for each partition. The reads are then “flowed” through a Bloom filter to dispatch the alignment task to the corresponding node(s). Finally, the reads are aligned on all partitions and the results are combined together to create the final output.

dida workflow

Citation

Mohamadi H, Vandervalk BP, Raymond A, Jackman SD, Chu J, et al. (2015) DIDA: Distributed Indexing Dispatched Alignment. PLoS ONE 10(4): e0126409. doi: 10.1371/journal.pone.0126409

 

Current Release
DIDA 1.0.1

Released Apr 24, 2015

This version introduces compression of intermediate files to reduce disk space requirements.
More about this release…

Download file Get DIDA for all platforms
Source code

All Releases

Version Released Description Compatibility Licenses Status
1.0.1 Apr 24, 2015 This version introduces compression of intermediate files to reduce disk space requirements. More about this release… BCCA (academic use) final
1.0.0 Feb 25, 2015 dida-wrapper, dida-mpi, and the batch versions are optimized. Fixed many portability issues and bugs, and improved some error messages. More about this release… BCCA (academic use)
BCCA (academic use)
BCCA (academic use)
final
0.1.3 Dec 13, 2014 Adding wrapper and fully streamlined versions of DIDA. More about this release… BCCA (academic use)
BCCA (academic use)
BCCA (academic use)
final
0.1.2 Jul 10, 2014 New merging step compatible with BWA, Bowtie, Novoalign, and ABySS-map with different merging strategies. More about this release… BCCA (academic use) final
0.1.1 0.1.1 More about this release… BCCA (academic use) pre-release
Project Resources

Project owner: Hamid Mohamadi