Bicolor: Bi-level error correction for PacBio long reads
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
default_parameters
LICENSE
Makefile
README.md
combine.cpp
iterative.cpp
muscle
runCombine.sh
runCorr.sh

README.md

Bicolor

Bi-level error correction for PacBio long reads

Compile

make all

Run

1. sh runCorr.sh
2. sh runCombine.sh

Tips

  1. GATB should be installed. Please see http://gatb-core.gforge.inria.fr. After installing, the variable GATB in the file Makefile is the path to search GATB.

  2. If errors occur when compiling GATB, the problem may be the version of G++.

  3. MUSCLE download from http://drive5.com/muscle. Even we provide an executable file of MUSCLE, it may not support your machine.

  4. When runs sh runCombine.sh, please make sure that sh runCorr.sh must finished. As muscle runs in multiple cores with command "&".

  5. When running the codes, names of long read file, short read file and output file can modified in the files runCorr.sh or runCombine.sh.


Declaration
Some parts of the codes are changed from LoRDEC and GATB library is used.

Status

Submitted to InCoB 2017.

Contacts

If any bugs during you run our code, please email to yyuanshengliu@gmail.com