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Instructions for scaffolding MIRA 454 contigs & 25 KB paired-end data with BAMBUS

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  • Instructions for scaffolding MIRA 454 contigs & 25 KB paired-end data with BAMBUS

    Regarding this paper and the command from this paper:
    sff_extract -l ../paired_end_adaptor.fasta F04Y2AI01.sff -i "insert_size:
    25000,insert_stdev:9000" -o non_0157

    How to get the paired_end_adaptor.fasta file?
    How to determine the insert_size and insert_stdev?
    Anybody can provide suitable links or sources to solve this two problem?
    Thanks a lot

  • #2
    You could ask on the MIRA mailing list - or at least search their archives,
    http://www.freelists.org/archive/mira_talk

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