SPADES is an assembly toolkit containing various assembly pipelines.

SPADES works with Illumina or IonTorrent reads, and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads.

SPADES supports paired-end reads, mate-pairs and unpaired reads. It can take as input several paired-end and mate-pair libraries simultaneously. SPADES was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPADES is not intended for larger genomes, such as mammalian size genomes. For such purposes, you use SPADES at your own risk.