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  • solid_denovo_postprocessor.pl removes velvet contig sequence.

    This question might be better directed to SOLID developers
    But I have a problem where my final basespace output I have just a fasta header and no sequence. Did the solid scripts remove it because of low quality?

    These are the last few steps.

    velvet_0.7.55/velvetg_de ./S4output_directory/ -read_trkg yes -amos_file yes

    solid_denovo_postprocessor.pl --afgfile ./S4output_directory/velvet_asm.afg --csfasta ./S4-output/colorspace_input.csfasta --run fragment --output ./sample4_input

    echo 'Running denovoadp'
    time denovoadp ./sample4_input 30000 > ./sample4_output


    so after step 1
    I get this in contigs.fa
    >NODE_780_length_22_cov_13.590909
    CCCCCCCCCCCCCCCCCACATGGCCGCGCCCCCCCCCCCCCC

    from step 2 onwards the contig has empty sequence i.e.
    >NODE_780-0
    >NODE_1882-0
    http://kevin-gattaca.blogspot.com/

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