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

  • From: "Wachholtz, Michael" <mwachholtz@xxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Mon, 15 Nov 2010 18:09:25 -0600

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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