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GitHub

Please visit the latest version at: https://github.com/aquaskyline/SOAPdenovo2

Citation

Please cite SOAPdenovo2 published in GigaScience http://www.gigasciencejournal.com/content/1/1/18/ Luo et al., SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler GigaScience, Vol. 1, No. 1. (2012), 18, doi:10.1186/2047-217x-1-18

Caveat for Mac user

Mac version r240 tested with 200x Yeast genome simulated reads using 63mer on Mac OS X Maverick 10.9.1 on a Late 2013 Macbook Pro with 16G memory. Theoretically the program should work with all 10.9 subversions. I don't have a change to test it with old OS versions including 10.8 and 10.7, as well as Mac OS X Server, so please kindly write to me if you've succeeded running the program in your Mac settings other than mine.

Note that the memory compression feature in Maverick 10.9 kicks in uncontrollably and in turn speeds down the program and makes the machine peroidically unresponsive. If you use SOAPdenovo2 frequently on your Mac please consider switch off the memory compression feature by running following command in terminal and restart: sudo nvram boot-args="vm_compressor=1"

Source: README.md, updated 2015-03-17