Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data.
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ABSTRACT:
SUBMITTER: Sadedin SP
PROVIDER: S-EPMC6472072 | biostudies-literature | 2019 Apr
REPOSITORIES: biostudies-literature
Publications
Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data.
Sadedin Simon P SP Oshlack Alicia A
Genome biology 20190418 1
The vast quantities of short-read sequencing data being generated are often exchanged and stored as aligned reads. However, aligned data becomes outdated as new reference genomes and alignment methods become available. Here we describe Bazam, a tool that efficiently extracts the original paired FASTQ from alignment files (BAM or CRAM format) in a format that directly allows efficient realignment. Bazam facilitates up to a 90% reduction in the time for realignment compared to standard methods. Ba ...[more]
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