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[Seqan-dev] question about mason

<-- thread -->
<-- date -->
  • From: Sonia Vivas <vivas@molecularhealth.com>
  • To: <seqan-dev@lists.fu-berlin.de>
  • Date: Wed, 24 Oct 2012 17:10:57 +0200
  • Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
  • Subject: [Seqan-dev] question about mason

Hi!
I'm using seqan mason to generate mate pairs reads:

./build/Release/core/apps/mason/mason illumina -i -s $i -N 10000000 -n 50 -mp -hM 8 -hnN -o ./reads.fa ./fake_patient.fasta

I do not need the sam file as output, is there any way of avoiding that is generated? ( I didn't find any option...) I need high coverage, therefore the 10 million reads. This is taking a lot of time and memory (50 minutes and up to 30Gb), is there a reason for this to take so much memory? am I doing something wrong? (my fasta file is 2.9Gb).

Thank you for your help,

--
Sonia Vivas




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  • Follow-Ups:
    • Re: [Seqan-dev] question about mason
      • From: "Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>
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