Pseudo-molecule

[Shlomo Blum]

Hi,

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

[westerman]

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.

[Ciaran]

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