AssemblerSPAdes plugin

The AssemblerSPAdes plugin is a de Bruijn graph assembler. The plugin breaks sequence reads into kmers of defined length, makes a connected graph, and traverses through that graph to produce contigs. The plugin report includes basic analysis metrics such as number of contigs, N50, length of the longest contig, and a downloadable FASTA file of the assembled sequences. The plugin assumes a haploid genome, and is ideal for genomes under 50 megabases in size. For multiploid genomes, reads from different copies of a chromosome tend to assemble into different contigs.

For de novo assembly, use a Generic Sequencing application Planned Run template for the Torrent Suite™ Software analysis.