[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: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 22 May 2014 21:23:00 +0200
On 22 May 2014, at 19:08 , Bayles, Darrell <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
Other related posts:
