FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy.

ABSTRACT:

Background

Storage of genomic data is a major cost for the Life Sciences, effectively addressed via specialized data compression methods. For the same reasons of abundance in data production, the use of Big Data technologies is seen as the future for genomic data storage and processing, with MapReduce-Hadoop as leaders. Somewhat surprisingly, none of the specialized FASTA/Q compressors is available within Hadoop. Indeed, their deployment there is not exactly immediate. Such a State of the Art is problematic.

Results

We provide major advances in two different directions. Methodologically, we propose two general methods, with the corresponding software, that make very easy to deploy a specialized FASTA/Q compressor within MapReduce-Hadoop for processing files stored on the dis

SUBMITTER: Ferraro Petrillo U 

PROVIDER: S-EPMC7986029 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature