Fq_delta - Efficient storage of processed versions of fastq files

Authors

  • Andra Veraart 1 School of Communication, Media and Information Technology, Rotterdam University, Rotterdam 2 Dept. Viroscience, Erasmus Medical Center, Rotterdam
  • Henk-Jan van den Ham Dept. Viroscience, Erasmus Medical Center, Rotterdam
  • Maarten A. Bijl Dept. Viroscience, Erasmus Medical Center, Rotterdam
  • Arno C. Andeweg Dept. Viroscience, Erasmus Medical Center, Rotterdam
  • Anita C. Schürch Dept. Viroscience, Erasmus Medical Center, Rotterdam

DOI:

https://doi.org/10.14806/ej.20.0.698

Keywords:

next generation sequencing, storage

Abstract

This technical note describes fq_delta, a python module and shell script that enables the storage of processed versions of fastq files generated by DNA and RNA sequencing technologies. By using Myer's diff algorithm to perform per-character comparisons between the original and processed fastq files, we generate delta files that describe the changes in the processed fastq file relative to the original file. While the delta files are only a fraction of the original size (0.1 – 3%), they allow lossless reconstruction of the processed fastq files. Depending on the number of processing steps, implementation of this module will lead to a significant reduction in storage required for processing sequence data.

Availability:

Fq_delta is available for download at https://github.com/averaart/fq_delta.

EMBnet.journal 20

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Published

2014-03-05

Issue

Vol. 20

Section

Technical Notes

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