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  • Pseudo-molecule

    Hi,

    How may I concatenate contigs into a single pseudo-molecule using a linker sequence? Does anyone know of a script for this purpose?

  • #2
    Well if you don't care about contig ordering then just put a bunch of 'N's (I suggest 100) between each contig. I'd probably use 'sed' for this. Something like:

    sed -e 's/>.*/NNNNNNNNNNNNNNNNNN/' <input.fasta>output.fasta

    Then reformat if desired (I used fasta_formatter) and put a header on top of the combined sequence.

    Comment


    • #3
      I'm not really sure i understand what you are asking for or why.

      but here is my take;

      cat contigs.fa | perl -p -e 's/^>.*/LINKER/g' | perl -p -e 's/\n//g' > Pseudo.fa

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