Fulcrum: condensing redundant reads from high-throughput sequencing studies.
MOTIVATION: Ultra-high-throughput sequencing produces duplicate and near-duplicate reads, which can consume computational resources in downstream applications. A tool that collapses such reads should reduce storage and assembly complications and costs. RESULTS: We developed Fulcrum to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.
Pubmed ID: 22419786
- Burriesci MS
- Lehnert EM
- Pringle JR
Bioinformatics (Oxford, England)
May 15, 2012
- Agency: NHGRI NIH HHS, Id: 5 T32 HG000044
- Agency: NHGRI NIH HHS, Id: T32 HG000044
- Gene Expression Profiling
- High-Throughput Nucleotide Sequencing
- Sequence Analysis, DNA