SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data.

ABSTRACT: Next-generation sequencing (NGS) technologies have led to a huge amount of genomic data that need to be analyzed and interpreted. This fact has a huge impact on the DNA sequence alignment process, which nowadays requires the mapping of billions of small DNA sequences onto a reference genome. In this way, sequence alignment remains the most time-consuming stage in the sequence analysis workflow. To deal with this issue, state of the art aligners take advantage of parallelization strategies. However, the existent solutions show limited scalability and have a complex implementation. In this work we introduce SparkBWA, a new tool that exploits the capabilities of a big data technology as Spark to boost the performance of one of the most widely adopted aligner, the Burrows-Wheeler Aligner (BWA)

SUBMITTER: Abuin JM 

PROVIDER: S-EPMC4868289 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature