Add linker sequence to the contig in a fasta file
git clone https://github.com/demis001/addLinkerSequence.git
cd addLinkerSequence
Add the add_linker_to_contigs.py to your PATH in .bashrc
PATH=$PATH:[full path to]/addLinkerSequence
To get help:
add_linker_to_contigs.py -h
To add the linker to the contigs in a fasta file:
add_linker_to_contigs.py test.fasta NNN > out.fa
To add the linker and join all contigs into a single sequence
add_linker_to_contigs.py test.fasta NNN --singleseq > out.fa
Generate concatinated pseudo Genome
grep -v ">" out.fa | tr -d "\t\n\r" > temp.fa
cat temp.fa | awk '{print ">out_pseudoGenome\n"$0}' > out_pseudoGenome_linker.fa && rm temp.fa