Fast and High Throughput Algorithm for PacBio Long Read Self-Correction
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README.md
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README.md

Overview

FLAS is software that makes self-correction for PacBio long reads with fast speed and high throughput.

Copy right

FLAS is under the Artistic License 2.0.

Short manual

  1. System requirements

    FLAS is suitable for 32-bit or 64-bit machines with Linux operating systems. At least 4GB of system memory is recommended for correcting larger data sets.

  2. Installation

    The MECAT software and Python(3.0+) are required to run FLAS.

    • The source files in 'src' folder can be complied to generate a 'bin' folder by running Makefile: make.
    • Put the 'bin' folders of MECAT and FLAS to your $PATH: export PATH=PATH2MECATbin:$PATH and export PATH=PATH2FLASbin:$PATH, respectively.
  3. Input

    • Long reads in FASTA format.
  4. Using FLAS

    FLAS long_reads.fasta [-options|-options]
    

    Options (default value):
    -c (100)
    Coverage of the long reads.
    -α1 (0.5)
    Fraction value to distinguish between the cases (i)/(ii) and (iii).
    -α2 (0.5)
    Fraction value to distinguish between the cases (i) and (ii).
    -β1 (0.05)
    Difference value of alignment identities to find the correct aligned path.
    -β2 (0.2)
    Difference value of expected amounts of aligned long reads to find the correct aligned path.

  5. Outputs

    • Error corrected trimmed long reads.
    • Error corrected split long reads.