metaSPAdes Assembly

SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. See the SPAdes home page for more info.

metaSPAdes can be run by the following command:

cd /mnt/WGS-data

metaspades.py -o metaspades_out --pe1-1 read1.fq --pe1-2 read2.fq

The contig sequences are located in the metaspades_out directory in file contigs.fasta. Again, let’s get some basic statistics on the contigs:

getN50.pl -s 500 -f metaspades_out/contigs.fasta