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Fqtools: an efficient software suite for modern FASTQ file manipulation.

ABSTRACT:

Unlabelled

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.

Availability and implementation

fqtools is open source and is available at: https://github.com/alastair-droop/fqtools

Supplementary information

Supplementary data are available at Bioinformatics online.

Contact

a.p.droop@leeds.ac.uk.

SUBMITTER: Droop AP

PROVIDER: S-EPMC4908325 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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fqtools: an efficient software suite for modern FASTQ file manipulation.

Droop Alastair P AP

Bioinformatics (Oxford, England) 20160218 12

<h4>Unlabelled</h4>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 ...[more]

PMID: 27153699

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