[mira_talk] Re: Filtering (size or quality) for Ion Torrent data
- From: Adam Witney <awitney@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 03 Aug 2012 09:51:17 +0100
Hi Nick,
Take a look at seqtk or sickle, these might do what you need:
https://github.com/lh3/seqtk/
https://github.com/najoshi/sickle
Adam
On 03/08/2012 08:41, Nicholas Heng wrote:
Hi Bastien and other MIRA-using Folk,
I have a dataset from an Ion Torrent 318 run that's about 480 Mb in size
(average readlength 177 bp). My underpowered 8 GB bioinformatics machine spent
7 solid days churning away at the data using MIRA 3.4 to no avail.
Can any of you next-gen sequencing gurus please suggest a program that would allow
me, one with absolutely no programming skill, to filter the dataset into say <150
bp and >150 bp subsets such that it's suitable for MIRA to handle? Alternatively,
a program that would sort by sequence quality... but this may be harder.
The bacterial genome I'm sequencing is de novo (no reference) and it's about 2
- 2.5 Mb in size. There is a 454 run being done but I'd like subsets of Ion
Torrent for a hybrid assembly with MIRA. And no, we can't afford a more
accurate Illumina or SOLiD run at the present time.
Any help is greatly appreciated.
Cheers,
Nick.
================================
Nicholas (Nick) C.K. Heng, Ph.D.
Department of Oral Sciences
Faculty of Dentistry
University of Otago
P.O. Box 647
Dunedin 9054
NEW ZEALAND.
Ph: +643 4799254
Fx: +643 4797078
================================
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