SGA is a tool for de novo genome assembly and is capable of using short reads for assembly without the need for de Bruijn graph. This tool implements memory efficient data structures and algorithms based on FM-index from compressed Burrows-Wheeler transform. This assembler can error correct, assemble and scaffold sequenced data.
Simpson JT, Durbin R "Efficient de novo assembly of large genomes using compressed data structures." Genome Res. 2012 Mar;22(3):549-56. doi: 10.1101/gr.126953.111. Epub 2011 Dec 7. https://doi.org/10.1101/gr.126953.111
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