[mira_talk] Re: De novo assembly using Illumina and PacBio data aborts after internal error
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 24 Jun 2016 08:02:12 -0400
On 23 Jun 2016, at 14:08 , Bibi Lujan <bibilujan@xxxxxxxxx> wrote:
I am using MIRA (4.9.6) to assemble a plant genome (260MB) with illumina and
corrected PacBio data. However my assembly has aborted after the following
error:
Internal logic/programming/debugging error (sigh this should not have
happened)
• Alignment of two sequences: 81726 > 65530 bases, cannot handle,
shouldn't *
• have happened! *
I’ve had a couple of reports regarding that error in the past few weeks. In
short: this is a “won’t fix”.
I’d like to cite the following section from the MIRA manual:
1.4. For which data sets to use MIRA and for which not
As a general rule of thumb: if you have an organism with more than 100 to 150
megabases or more than 20 to 40 million reads, you might want to try other
assemblers first.
MIRA was *never* developed to handle large eukaryotic organisms and while some
people do abuse it for that with some success, it is not my goal to develop
MIRA with the current code base to make it reliable for that task.
May I suggest you try FALCON or canu?
Bastien
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