Convert an interleaved fasta file to a single line fasta using only the Linux command line

Most databases provide biological sequences in the multiline fasta format. On the commandline however it is a lot easier to work with a fasta file where the sequence spans just a single line.

The following command snippet allows you to convert you the interleaved format to the single line format using awk, which is installed on most Linux systems by default.

awk '{if(NR==1) {print $0} else {if($0 ~ /^>/) {print "\n"$0} else {printf $0}}}' interleaved.fasta > singleline.fasta

Receive updates about NGS articles and trainings

Share this article

Last updated on April 26, 2018

ecSeq is a bioinformatics solution provider with solid expertise in the analysis of high-throughput sequencing data. We organize public workshops and conduct on-site trainings on NGS data analysis.

Would you like to receive updates about our NGS trainings and solutions? Then sign-up for our newsletter