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SPAdes is an assembly toolkit containing various assembly pipelines.

Assembling a genome from Illumina paired-end reads using SPAdes

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…

  1. -1 is the file with forward reads.
  2. -2 is the file with reverse reads.
  3. -t or --threads sets the number of processors/threads to use. The default is 16.
  4. -m or --memory is memory the limit in Gb. SPAdes terminates if it reaches this limit. The default value is 250Gb.
  5. -o or --outdir is the output directory to use. The default is the current directory.

SPAdes supports uncompressed (.fastq or .fq) or compressed (.fastq.gz or .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.

See also

Further reading