<![CDATA[BOL: Cactus: a reference-free whole-genome multiple alignment program]]> https://bioinformaticsonline.com/bookmarks/view/39837/cactus-a-reference-free-whole-genome-multiple-alignment-program? https://bioinformaticsonline.com/bookmarks/view/39837/cactus-a-reference-free-whole-genome-multiple-alignment-program Mon, 12 Aug 2019 07:52:33 -0500 https://bioinformaticsonline.com/bookmarks/view/39837/cactus-a-reference-free-whole-genome-multiple-alignment-program <![CDATA[Cactus: a reference-free whole-genome multiple alignment program]]> Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111

Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should expect Cactus to use approximately 120 CPU-days of compute per genome, with about 120 GB of RAM used at peak. The requirements scale roughly quadratically, so aligning two 1-megabase bacterial genomes takes only 1.5 CPU-hours and 14 GB RAM. 

Address of the bookmark: https://github.com/ComparativeGenomicsToolkit/cactus

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