fqtools: an efficient software suite for modern FASTQ file manipulation.
Where this comes from
- Record sourced from PubMed, PMID 27153699.
- Also identified by DOI 10.1093/bioinformatics/btw088 and PMC identifier 4908325.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Many Next Generation Sequencing analyses involve the basic manipulation of input sequence data before downstream processing (e.g. searching for specific sequences, format conversion or basic file statistics). The rapidly increasing data volumes involved in NGS make any dataset manipulation a time-consuming and error-prone process. I have developed fqtools; a fast and reliable FASTQ file manipulation suite that can process the full set of valid FASTQ files, including those with multi-line sequences, whilst identifying invalid files. Fqtools is faster than similar tools, and is designed for use in automatic processing pipelines. fqtools is open source and is available at: https://github.com/alastair-droop/fqtools Supplementary data are available at Bioinformatics online. a.p.droop@leeds.ac.uk.
Medical subject headings
- Software