[mira_talk] Re: Solexa paired ends and 454 single reads
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 21 Jan 2010 10:16:34 +0100
Hi Mihaela,
I've been running such an assembly. Whereas the 454-only (~300k reads)
assembly took a few hours, adding ~500k Solexa paired-end reads made
it about 8 days... I think this is due to the fact that building
contigs is highly time-consuming in MIRA, and Solexa reads assemble in
a lot of small contigs.
You can check what Pass MIRA is in:
grep "Pass" assembly.log
As far as I remember, MIRA does 5 passes when set with accurate.
By the way, how many reads of each kind do you have?
Cheers,
Lionel
On 21 Jan 2010, at 10:08 , Mihaela Angelova wrote:
Hello,
I want to use Mira for assembly of 454 reads combined with solexa
paired end reads. However, the assembling was started two days ago
with:
mira -project=pp -job=denovo,genome,accurate,454,solexa -GE:amm=no
SOLEXA_SETTINGS -GE:tismin=2500:tismax=3500
and still hasn't finished. I have noticed that a huge number of
paired ends were discarded because they were too short :
AAA/2 too small even with paired end
Is this because their ends might have been clipped. In the
project_int_clippings.0.txt there are messages like :
proposed cutback 1b: left AAA/2 9 -> 24
If I use the noclipping command, would it make the run more
accurate? Is it normal that the run takes more than two days (if i
need half a day to assemble the 454 reads without the paired ends)?
Thanks a lot,
Mihaela
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Lionel Guy
Thunmansgatan 25, SE-75421 Uppsala
phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy.lionel@xxxxxxxxx
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