[mira_talk] Re: large hybrid assembly w/ minimal ram

  • From: Sven Klages <sir.svencelot@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Tue, 16 Nov 2010 21:55:20 +0100

oh, yes. I see, .. I just wanted to use it for my own data and was quite
astonished ;-)
fasta output, no qualities ... not of any use for me neither ..

cheers,
Sven

2010/11/16 Wachholtz, Michael <mwachholtz@xxxxxxxxxxx>

> I have, but the output is in fasta format with no quality scores. The
> only advantage this program has is that it will output how many
> identical reads there were. I prefer the fastq program in that it will
> retain the quality score of best sequence and will output in fastq
> format.
>
> On Mon, Nov 15, 2010 at 5:18 AM, Sven Klages
> <sir.svencelot@xxxxxxxxxxxxxx> wrote:
> > Hi Michael,
> >
> > 2010/11/15 Wachholtz, Michael <mwachholtz@xxxxxxxxxxx>
> >>
> >> [...]
> >>
> >> it is safe to use such strict criteria. After that, for each lane, we
> >> used the fastq program to collapse/remove any identical reads. This
> >
> > [...]
> >
> > just a short question. You have successfuly used the FASTX-Toolkit to
> > quality-clip your data;
> > this tool collection also contains a program to remove duplicates from
> NGS
> > data:
> >
> > FASTQ/A Collapser
> > Collapsing identical sequences in a FASTQ/A file into a single sequence
> > (while maintaining reads counts)
> >
> > Have you tried this for your data?
> >
> > cheers,
> > Sven
> >
> >
>
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