SPAdes can be used to assemble paired-end reads as follows:
$ spades -1 reads_1.fq.gz -2 reads_2.fq.gz -t 5 -m 200 -o results/directory/
In this command…
-1is the file with forward reads.
-2is the file with reverse reads.
--threadssets the number of processors/threads to use. The default is 16.
--memoryis memory the limit in Gb. SPAdes terminates if it reaches this limit. The default value is 250Gb.
--outdiris the output directory to use. The default is the current directory.
SPAdes supports uncompressed (
.fq) or compressed (
.fq.gz) sequencing read inputs. In the output directory, the assembled genome will be available as contigs (
contigs.fasta) and scaffolds (
scaffolds.fasta), both of which are FASTA nucleotide files.