[mira_talk] new version 2.9.45 and solexa

Hi Bastien and all,

I started new mira run yesterday night, it is mapping of solexa
mate-pairs paired-end 36nt on 454 contigs produced by mira.

I have two questions:

Previous versions of mira did not recognized solexa naming scheme (/1
/2), I had to rename all reads (using .r .f). Now it seems mira can use
the original naming scheme? Can also .r.f scheme be used for solexa reads?

Also quality score previously used by mira was phred score. Now it looks
mira can use solexa quality scoring as well. Am I right? What is the
default? Is it possible to explicitly tell mira which scoring scheme
should be used? Because both schemes are very similar, can we expect no
big changes in assembly?

My first impression is, that mapping with new version is very slow.

for a contig of the size 3.3k and average coverage of solexa reads 10x
it took 25 minutes:

<code>
Building new contig 1
Localtime: Wed May 13 03:50:54 2009
Unused reads: 13471594
...
-------------- Contig statistics ----------------
Contig id: 1
Contig length: 3314
...
done.
Localtime: Wed May 13 04:15:21 2009
</code>

these are parameters I used for mapping:

<code>
mira
-project=mi_v8 -job=mapping,genome,solexa,normal
COMMON_SETTINGS
-GE:not=16:uti=on:tismin=2300:tismax=2700
-SB:lb=on:sbuip=1:bft=caf
-AS:nop=3 -DP:ure=on -ED:ace=off
-SK:mnr=on:bph=14:hss=4
SOLEXA_SETTINGS
-GE:uti=on:tismin=2300:tismax=2700
</code>

Because assembly of 454 reads by mira produced several thousands of
contigs (454 coverage 10x, genome is eucaryote with expected size
~100M), this speed is too slow for real life usage.

Thanks,

Jan


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