[mira_talk] Re: MIRA 4.0.2 Aborted
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 14 Jul 2016 12:10:13 -0400
On 14 Jul 2016, at 10:34 , Peter Lannoo <pjl228@xxxxxxxxxxx> wrote:
I've been working on my first Ion Torrent genome assembly, and Mira seems to
be the best option for me since I have a Mac computer. I'm running MIRA 4.0.2
on a Macbook Pro laptop, Version 10.11.1 with an 8 GB 16 MHz DDR3 memory.
I've been attempting to assemble a frog genome (~2.3 gb, 69771595 total
sequences according to FASTQC) both de novo and mapping. However, I keep
having the same problem on both analyses:
I’ll try to be gentle :-)
1. de-novo assembly (or even mapping) of an eukaryotic genome on a machine with
8 GiB is an idea you should get out of your head. Now! For de-novo (do NOT take
MIRA for this, it’s not made for that) you will need a couple of dozen GiB,
maybe up to a low 3-number. Also if you do a mapping with MIRA (which I do not
recommend).[*]
2. You sure you have enough coverage? Even if I assume a very small genome of
250 Mb and MiSeq with 250 usable bp, I get nowhere near the 60-80x coverage I’d
like to see for a de-novo.
Bastien
[*] If you are memory constraint, you can give “Minia” a try. Though general
consensus is that it’s more of a proof-of-concept.
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