Blue

The software tool 'Blue' is an error-correction algorithm that corrects sequencing errors in both FASTQ and FASTA formats. It is based on k-mer consensus and context, and can correct substitution, deletion, insertion errors, as well as uncalled bases. Blue is memory-efficient, scalable, and faster than other published tools, making it suitable for use on large sequencing datasets. It can be used to correct one dataset with the consensus derived from another dataset, and is compatible with downstream tools that depend on read pairing.

Topic

DNA;Sequencing;Genomics

Detail

  • Operation: Sequencing error detection

  • Software interface: Command-line user interface

  • Language: C#

  • License: MIT License

  • Cost: Free

  • Version name: v2.2

  • Credit: The CSIRO Transformational Biology Capability Platform

  • Input: FASTA, FASTAQ

  • Output: -

  • Contact: Paul.Greenfield@csiro.au

  • Collection: -

  • Maturity: Stable

Publications

  • Blue: correcting sequencing errors using consensus and context.
  • Greenfield P, et al. Blue: correcting sequencing errors using consensus and context. Blue: correcting sequencing errors using consensus and context. 2014; 30:2723-32. doi: 10.1093/bioinformatics/btu368
  • https://doi.org/10.1093/bioinformatics/btu368
  • PMID: 24919879
  • PMC: -

Download and documentation

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