In order to add some sequences as "contaminants database" in the fastqc analysis, a contaminant file should be provided with the following format: header[tabulation]sequence. Usage: fasta2oneline.sh example.fa > contaminants.txt

fasta2oneline.sh

#!/bin/bash

# fasta2oneline.sh

# Convert fasta file in one line: header[tab]sequence (useful for fastqc contaminant file, for example)
# Output to the stdout, redirect it to a file
# Usage: fast2oneline.sh x_example.fa > z_contaminants.txt

INPUT_FILE=$1
cat ${INPUT_FILE} | sed '/^$/d' | sed -n '/^>/!{H;$!b};s/$/ \t/;x;1b;s/\n//g;p'

x_example.fa

>seq1
catcgatcgtacgatcgtacgtacgtagc

>seq2
acgtacgtcatgcatgatactgtagctacgtacgtacgt

>seq3
agctagtcgatcgatcgatcgatcgatcgatcgatcgtacgtacg

z_contaminants.txt

>seq1   catcgatcgtacgatcgtacgtacgtagc
>seq2   acgtacgtcatgcatgatactgtagctacgtacgtacgt
>seq3   agctagtcgatcgatcgatcgatcgatcgatcgatcgtacgtacg