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  • Failure of transforming Velvet .afg file into GDE .contig file

    I did a hybrid assembly using Velvet. There were three typs of data, Solexa, 454 and sanger data. Then I wantted to scaffold the contigs using Bambus. I have to transform velvet_asm.afg file into GDE .contig file .

    First tansform .afg to AMOS bank file
    'bank-transact -m velvet_asm.afg -b velvet_amos.bank -c'

    Second transform AMOS bank file into .contig file
    'bank2contig velvet_amos.bank >velvet.contitg'

    The first step was ok. The second step fail.
    Error returned:
    'ERROR: -- Fatal AMOS Exception --
    WHAT: Invalid sequence subrange
    LINE: 90
    FILE: Sequence_AMOS.cc

    '

    Who can tell me the reason and how to resolve it? Thank You!
    github:
    https://github.com/Bioinformatics-and-Genomics

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