We are using PCAP and Arachne to assembly Daphnia pulex (crustacean) and compare/refine the JGI JAZZ assembly of this water flea. Arachne is still designed mostly for 1-cpu, but PCAP (and newer variant PCAPrep) is designed for cluster/grid usage, although it has 1 step where most of the work needs to be done on 1-cpu with all data in memory. See some info in this proposal: http://iubio.bio.indiana.edu/biogrid/teragrid-genomics06-proposal.pdf We are using TeraGrid for most of the cpus, including running Arachne at rachel.PSC.teragrid.org with its alpha processors. X. Huang, the author of PCAP, needed to provide us some small software adjustments to run on the NCSA TeraGrid IA64 cluster (something about mismatched system libraries with his binary release), PCAP's parallel parts work mainly as a set of independent processes (don't recall if it uses MPI or not). By the way, I'm working on general methods to use Grid systems, esp. US TeraGrid as a replacement for maintaining your own local clusters in genome analyses. Anyone interested in using such methods, please feel free to contact me. In terms of assembly quality for Daphnia (about 200MB genome), in our hands Arachne provides bigger, fewer scaffolds, but we are not yet sure if they are a better assembly. PCAP has generated more, smaller ones. Daphnia has 12 chromosomes, we get a few thousand scaffolds from Arachne, and 10,000s of scaffolds from PCAP, for this 9X WGS data set. - Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gilbertd at indiana.edu -- http://marmot.bio.indiana.edu/