CoLoRMap

Installation

In order to install CoLoRMap, you should first fetch the source code from CoLoRMap git repository.

git clone --recursive https://github.com/sfu-compbio/colormap.git

After obtaining the code, you need to install the dependencies. CoLoRMap uses BWA, SAMtools, and Minia. In order to build these dependencies, change to the source directory colormap and use make deps command.

cd colormap
make deps

At last, you can compile CoLoRMap binaries simply by running make command.

make

Correcting long reads

To correct long reads, you can use runCorr.sh script:

./runCorr.sh <pacbio.fasta> <illumina.fastq> <outPrefix> <threads>

After finishing this, the corrected long reads are stored in <outPrefix>_corr.fasta file in <outPrefix> directory.

Improving the correction using One-End Anchors (OEAs)

The script runOEA.sh can be used to further improve the quality of corrected long reads by using One-End Anchors (OEAs) to extend the borders of the corrected regions.

./runOEA.sh <pacbio_corr.fasta> <illumina.fastq> <outPrefix> <threads>

When this is done, the corrected long reads are stored in <outPrefix>_oea.fasta file in <outPrefix> directory.

Pulication

CoLoRMap: Correcting Long Reads by Mapping short reads
Haghshenas E, Hach F, Sahinalp SC, Chauve C
Bioinformatics. 2016 Sep 1;32(17):i545-i551. doi: 10.1093/bioinformatics/btw463

Contact

Please report problems and bugs on issues page. Otherwise, contact ehaghshe[at]sfu[dot]ca