[mira_talk] Re: Total consensus length is double ?
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 9 Jul 2010 12:44:13 +0200
Hi Jan,
From your plot it seems that you have a lot of very small contigs
that are non aligned. These are likely to be spurious. I would
recommend filtering out these. As a rule of thumb, any contig that is
slightly longer than the read length and has a coverage lower than 1/3
or 1/2 of the average coverage may be discarded.
You can use convert_project to do that. With an assembly of 454
Titanium data (read length ~400) and ~60X average coverage, I use
convert_project -f caf -t caf -x 500 -y 20 raw_assembly.caf
filtered_assembly
On 9 Jul 2010, at 11:39 , Jan van Haarst wrote:
Dear All,
I'm working on some benchmarks of assemblers[1], and one of those is
MIRA.
For that purpose, I have downloaded 3 datasets [2], and put those
into MIRA after using sff_extract.
I have run the assembly using the parameters as mentioned on the
MIRA website :
mira --project=$PROJECT --job=denovo,genome,accurate,454
I have used mira_3.2.0rc1_dev_linux-gnu_x86_64_static for this.
What I see is that the resulting consensus is twice the size of the
reference E. coli genome !
If I do a mummerplot of the consensus versus the reference
(hopefully attached), I see that the complete reference is present,
but also a lot of other data.
I would like to know what I can do to get MIRA to give about the
same (or better) results than newbler or CABOG using this dataset.
--
Dag,
Jan
[1] https://wiki.nbic.nl/index.php/Raw_results_of_NGS_de_novo_assembly
[2] ENA SRR00086ENA SRR000870ENA SRR001028
<mira_vs_reference_filtered_SNP.png>
============================================
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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