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BEETL-fastq: a searchable compressed archive for DNA reads.
Janin, Lilian; Schulz-Trieglaff, Ole; Cox, Anthony J.
Afiliação
  • Janin L; Computational Biology Group, Illumina Cambridge Ltd., Little Chesterford, Essex CB10 1XL, UK.
  • Schulz-Trieglaff O; Computational Biology Group, Illumina Cambridge Ltd., Little Chesterford, Essex CB10 1XL, UK.
  • Cox AJ; Computational Biology Group, Illumina Cambridge Ltd., Little Chesterford, Essex CB10 1XL, UK.
Bioinformatics ; 30(19): 2796-801, 2014 Oct.
Article em En | MEDLINE | ID: mdl-24950811
ABSTRACT
MOTIVATION FASTQ is a standard file format for DNA sequencing data, which stores both nucleotides and quality scores. A typical sequencing study can easily generate hundreds of gigabytes of FASTQ files, while public archives such as ENA and NCBI and large international collaborations such as the Cancer Genome Atlas can accumulate many terabytes of data in this format. Compression tools such as gzip are often used to reduce the storage burden but have the disadvantage that the data must be decompressed before they can be used. Here, we present BEETL-fastq, a tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. Importantly, the full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input.

RESULTS:

We show that 6.6 terabytes of human reads in FASTQ format can be transformed into 1.7 terabytes of indexed files, from where we can search for 1, 10, 100, 1000 and a million of 30-mers in 3, 8, 14, 45 and 567 s, respectively, plus 20 ms per output read. Useful applications of the search capability are highlighted, including the genotyping of structural variant breakpoints and 'in silico pull-down' experiments in which only the reads that cover a region of interest are selectively extracted for the purposes of variant calling or visualization. AVAILABILITY AND IMPLEMENTATION BEETL-fastq is part of the BEETL library, available as a github repository at github.com/BEETL/BEETL.
Assuntos

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Análise de Sequência de DNA / Compressão de Dados / Neoplasias Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2014 Tipo de documento: Article País de afiliação: Reino Unido

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Análise de Sequência de DNA / Compressão de Dados / Neoplasias Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Revista: Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2014 Tipo de documento: Article País de afiliação: Reino Unido