[mira_talk] Re: MIRA v. 3.9.15 vs MIRA v. 4.0.2 performance degradation issues when using Illumina 54-bp paired-end reads in hybrid assembly
- From: "Bayles, Darrell" <Darrell.Bayles@xxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 22 May 2014 19:41:14 +0000
The bacterium does have a large number of large repetitive elements, and yes
most are transposons. We have considered PacBio and that would be the simplest
way to work through the big repeats; however, I'd still like to get some
clarification regarding the questions of performance differences between MIRA
v. 3.9.15 and MIRA v. 4.0.2, and clarification about the questions resulting
from your comments about short reads. While I didn't expect there to be a big
improvement in assembling with v. 4.0.2, I certainly didn't expect a
substantial decline in the goodness of assembly either.
Regards,
Darrell
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On
Behalf Of Bastien Chevreux
Sent: Thursday, May 22, 2014 2:23 PM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: MIRA v. 3.9.15 vs MIRA v. 4.0.2 performance
degradation issues when using Illumina 54-bp paired-end reads in hybrid assembly
On 22 May 2014, at 19:08 , Bayles, Darrell
<Darrell.Bayles@xxxxxxxxxxxx<mailto:Darrell.Bayles@xxxxxxxxxxxx>> wrote:
[...]
Any additional thoughts or suggestions are appreciated!
Hmmm I do have a suggestion, but you may not like it: ditch the data you have
atm and get your bug sequenced with PacBio (100x, better 200x) and assembled by
the sequencing provider. Maybe ask them to also deliver you the corrected
PacBio reads as MIRA often is able to close to a single contig where HGAP gave
you back a couple of contigs.
Reason I am saying this: you seem to have a nastier bug with, I'd guess, a
non-negligible number of repetitive elements (transposons probably). And
honestly ... your time and efforts are worth much more than the USD 2000 to
3000 you may have to pay to get it with PB.
Best,
Bastien
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