[mira_talk] Re: MIRA run failing due to megahubs
- From: Martin MOKREJŠ <mmokrejs@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 25 Jun 2014 19:39:29 +0200
Andreas Leimbach wrote:
> Hi Victoria,
>
> if you're new to NGS stuff, a nice tool for you probably is PRINSEQ, which
> combines QC and the option to trim/filter your data:
> http://prinseq.sourceforge.net/index.html
>
> Alternatively, for QC, the great FastQC:
> http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Useless for mira assemblies, I think Bastien can tell you more on this.
>
> Trimmomatic is also very popular for adapter removal soft clipping/trimming
> etc:
> http://www.usadellab.org/cms/index.php?page=trimmomatic
But it leaves in some dozens or hundreds of contaminated reads even with loose
settings and
overly "redundant" query database (input was say 80M reads). After you remove
them manually
and feed the data into mira, it will still find even hundreds of thousands of
adapters and
drop them in its initial pre-assembly steps.
If you rely completely on mira as Bastien suggests there will be some adapters
left
in contigs. So, I go via trimmomatic, manual cleanup, mira to get hopefully
clean assembly.
>
> For rRNA removal I do like SortMeRNA:
> http://bioinfo.lifl.fr/RNA/sortmerna/
>
> HTH,
> Andreas
Martin
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
