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Old 05-05-2011, 05:04 AM   #3
sphil
Senior Member
 
Location: Stuttgart, Germany

Join Date: Apr 2010
Posts: 192
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Hey,

first of all you are right. Due to massive amount of flags mira is using its hard to come up with. Here, http://mira-assembler.sourceforge.ne...e_library_size, you can find a very nice description on how to assemble paired end reads. Nevertheless i would recommend to subscribe at mira mailing list. The are really fast and even Bastien tries to help as much as he can (if the manual doesn't work out)...
Only havin' a slight look i would say you need to concate your files into one.
Then just start assembly with:
mira
--project=XXXXX
--job=denovo,genome,accurate,solexa
SOLEXA_SETTINGS -GE:tismin=250:tismax=750
>&log_assembly.txt


accurate means that you will have to wait until sun burns out so i would change it to draft for a first shot.

SOLEXA_SETTINGS -GE:tismin=250:tismax=750 , means that your insert size is 500bp.... everything else might be quite ok with defualt solexa settings

best,

philip
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