MeCorS

Metagenome-enabled error correction of single cell sequencing reads

Installation

git clone https://github.com/metagenomics/MeCorS.git
cd MeCorS && make

Usage

mecors [options] -s <SC.fastq> -m <MG.fastq>

-s <SC.fastq>  single cell sequencing reads
-m <MG.fastq>  metagenomic sequencing reads
               (fastq or fasta, can be gzip'ed)

-k INT         k-mer size for error correction [31]
-c INT         min. coverage in the metagenome [2]

-t INT         number of threads [16]
-B NUM         process ~NUM bp in each batch [100M]
-v             be verbose

Citation

MeCorS: Metagenome-enabled error correction of single cell sequencing reads
Andreas Bremges, Esther Singer, Tanja Woyke, Alexander Sczyrba
Bioinformatics (2016) doi:10.1093/bioinformatics/btw144

====== Heavily relies on on klib. Source code in part adopted from – or inspired by – Heng Li.