Spades is a genome assembler which intended for both standard isolates and single-cell MDA bacteria assemblies.
Parent program: spades
SPAdes is a genome assembler for small genomes. It was designed for single cell and multi-cells bacterial or fungal data sets. At the first computational stage SPAdes constructs the initial de Bruijn graph using k-mers. On the following stages the approach provides the improvement operations based on coverage, sequence lengths and graph structure to overcome technical problems of single cell data sets. The current version of SPAdes is compatible with Illumina and IonTorrent. It supports paired-end read, mate-pair and unpaired libraries, which can be used simultaneously.