Frank1eJohnson / FLAS

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

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.