Filter contig fasta file by GC content

Question

[victoriahristovaa]

Hello!

I have a de novo built contig file (contigs.fasta), assembly is done in SPAdes. From this file, I need to extract only the node sequences which have GC content below a certain % (e.g. extract all the node sequences that have GC content < 35%).

Do you have any suggestions of how I can do this? I am currently using seqkit to show me the GC content % of each node:

 seqkit fx2tab --name --only-id --gc contigs.fasta > results.txt

The problem is, this way I can only see GC% of each node, and cannot do any "extraction" of the actual node sequences I need.

Thank you very much in advance!

Answer 1

[GenoMax]

Try the following.

seqkit fx2tab --name --only-id --gc contigs.fa | awk -F "\t" '{if ($2 < 35) print $1}' | xargs -n 1 sh -c 'seqkit grep --pattern "$0" contigs.fa' > results.fa