[mira_talk] 454Ti, MiSeq250PE, HiSeq100PE Hybrid assembly..
- From: raw937@xxxxxxxxx
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sun, 5 May 2013 21:59:29 +0000
Hello again,
I have a few metagenomes were I have data with all three platforms.
I have filtered the reads for low quality, phiX, dimers etc.
What are the command parameters for such an assembly? I have them still in
fastq format.
I have 20million HiSeq100PE, 2million MiSeq250PE and a million 454Ti for about
8 samples. How much memory will I need? And, how many trends should I give
mira? As I want to assemble it rather quickly.
Cheers
Rick
Sent from my “contract free” BlackBerry® smartphone on the WIND network.
-----Original Message-----
From: Bastien Chevreux <bach@xxxxxxxxxxxx>
Sender: mira_talk-bounce@xxxxxxxxxxxxx
Date: Sun, 5 May 2013 23:37:49
To: <mira_talk@xxxxxxxxxxxxx>
Reply-To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: 454/PacBio hybrid & PacBio mapping assemblies with Mira
On May 5, 2013, at 23:32 , Stephen LeGrande <stlegrande@xxxxxxxxx> wrote:
> While mapping assemblies using long contigs as backbones and 454 sequences as
> short reads generally work fine - until now, I have been unable to map PacBio
> reads onto the same backbones - even when using just one single contig as
> reference.
> […]
> Mira quits with core dump every times at this point. This only happens with
> PacBio reads.
Uncool, looks like a real bug which survived several years in some main MIRA
modules without being triggered … because core dumps I track down whenever I
encounter them.
Would it be possible to get the data for me to go on a hunt?
Best,
Bastien
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