for illumina SOAP denovo.
Meraculous i have used which gives good result and is less memory intesive.
then u can use RAY.
meraculous is latest assembler which is working good , we can control the amount of ram used and tread in it, so far i m finding it out very good. other which is SGA which stood 3rd on assemblathon behind allpath and soap . you can try that here is one usefull link http://gage.cbcb.umd.edu/
for polishing 454 by illumina you can try mira. use 454 for denovo assembly and illumina for mapping it is done by mira. i have to look into it , as i remember i have done this before. i havent been able to run allpath , not enough suport or manual is avilable whch can clear hwo to run.
if you have 128 GB RAm then u can assemble 250-300 MB genome size organism . after that we r unable to assemble large genome. but if u try meraclous it will do also SGA is also good and MSR-CA
hmm.. mira, i think BWA better.
is there any software can use illumina consensus to create fake 454 reads ? Read from paper but sofware not listed.
allpath need two input file, one is "jumper reads", it can not work with single library input.
MSR-CA is modify version of celera Assembler 6.1, CABOG is 7.1.
The computer I use only hv 12GB RAM and single quadcore >.< Straight away heng for yeast illumina data assembly.
by the way, do you know how to use SSpace basic for extension scaffolding, bcoz i failed to make the progamme able to use the input reads to extend the scaffold.
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