[mira_talk] Re: assembly options for non-redundant contigs
- From: Laurent Manchon <lmanchon@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 03 Jun 2009 21:08:00 +0200
-- Richard,
which parameters do you use with cap3 ?
In the past i have made test to compare results from Mira and Tgicl
(TIGR software using cap3)
and as you said the results performed by Tgicl were very different in
quality and quantity (less contigs than Mira).
But to assemble 450000 cDNA reads cap3 need a lot of memory, and i had
always segmentation fault.
So, today i use Mira which is able to treat big input. Many others
assembler programs exist and it takes too much
time to compare them each others to establish which is the best.
Laurent --
Richard Gregory a écrit :
Hi Laurent,
Thanks for the suggestion. Have tested your options on the
pre-Titanium dataset, which I'm using as the benchmark because I have
an assembly using V2.6.15 to compare to. Extending the table from my
previous email:
number total number of
of reads bases contigs
169796 2865603 8540 V2.9.15
149758 6167756 24376 V2.9.43
132790 6409873 25099 V2.9.43_Laurent
Looking at contigs >500 bp, V2.9.49 with your options produced 1269
contigs, slightly fewer than the V2.9.49 options I was using.
The real test as far as I'm concerned is reassembly with something
else, such as cap3. Do the contigs assembly or are the kept separate.
For this V2.9.15 is easily the least redundant.
Mira Mira Cap3
Contigs Contigs Contigs
In Used Out
8540 2277 630 V2.9.15
24376 17545 1167 V2.9.43
25099 18261 1146 V2.9.43_Laurent
Richard
Laurent MANCHON wrote:
-- Hi Richard,
this is the commandline i use with 454 cDNA Titanium sequences (with
Mira 2.9.43):
mira -project=myproject -job=denovo,est,normal,454 -SK:mnr=yes
-SK:rt=4 -GE:not=2 -CO:asir=yes -CO:mr 454_SETTINGS
-AL:mrs=95:egp=yes:egpl=reject_codongaps:megpp=100 -LR:mxti=no
-CO:rodirs=10 -AL:mo=60 -CL:cpat=yes
input: 434802 sequences
output: 51559 contigs and 197939 singlets
Laurent --
Richard Gregory a écrit :
Hi All,
We been using Mira for a while now, handles cDNA much better than
Newbler and gives us more confidence in the result.
The latest batch of data is proving to be a problem, the current
project requires contigs that contain all similar reads and not be
split into multiple contigs of minor (or maybe large) differences.
We are having trouble finding the options to achieve this. Does
anybody know if/how this can be done?
The sequence data is 1.5 plates of 454 Titanium cDNA and half a
plate of pre-Titanium cDNA. Have tried many options, genome or est,
--noclippings, -SK:mmhr=1, -DP:ure=no, -AS:ard=no, -AL:egp=no,
-AS:sd=no, -CO:mr=no, -AL:mrs=55, -SK:mnr=yes, -SK:hss=1:pr=70, but
the result is basically the same. The better option set was -fasta
-job=denovo,est,draft,454 --noclippings -SK:mmhr=1 -DP:ure=no
-AS:ard=no -AS:sd=no -GE:not=4 -SK:hss=1:pr=70 , but this was
marginally better and doesn't achieve the desired result.
The only clue comes previous assemblies with earlier versions of
Mira, which produced much less redundancy, ie, was ~8000 contigs,
now V2.9.43 produces ~18000. Mapping this onto a reference showed
~1500 contigs could be the same gene. Assembling the ~1500 contigs
with cap3 produced ~3 contigs, one containing hundreds of contigs.
Thanks,
Richard
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