Metagenome-enabled error correction of single cell sequencing reads
git clone https://github.com/metagenomics/MeCorS.git
cd MeCorS && make
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
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.