SCALCE

The software tool 'SCALCE' is designed to address the challenges of data management, storage, and analysis of high-throughput sequencing (HTS) data. SCALCE is a boosting scheme based on the Locally Consistent Parsing technique that reorganizes reads to achieve a higher compression speed and compression rate without using a reference genome. Tests indicate that SCALCE can improve the compression rate achieved through gzip by a factor of 4.19 when the goal is to compress reads alone, and the running time of SCALCE+gzip improves that of gzip alone by a factor of 2.09. SCALCE also provides the option to compress quality scores and read names in addition to reads themselves.

Topic

Genomics

Detail

  • Operation: Formatting

  • Software interface: Command-line user interface

  • Language: C

  • License: BSD 3-Clause "New" or "Revised" License

  • Cost: Free

  • Version name: v2.8

  • Credit: Natural Sciences and Engineering Research Council of Canada, Bioinformatics for Combating Infectious Diseases Project, Michael Smith Foundation for Health Research grants, Canadian Research Chairs Program, NIH.

  • Input: FASTQ

  • Output: -

  • Contact: inumanag@sfu.oh;fhach@sfu.oh

  • Collection: -

  • Maturity: Mature

Publications

  • SCALCE: boosting sequence compression algorithms using locally consistent encoding.
  • Hach F, et al. SCALCE: boosting sequence compression algorithms using locally consistent encoding. SCALCE: boosting sequence compression algorithms using locally consistent encoding. 2012; 28:3051-7. doi: 10.1093/bioinformatics/bts593
  • https://doi.org/10.1093/bioinformatics/bts593
  • PMID: 23047557
  • PMC: PMC3509486

Download and documentation

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