Jit
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FASTQ to FASTA
By Jit 842 days ago
# bash
cat INFILE.fastq | paste - - - - |cut -f 1, 2| sed 's/@/>/'g | tr -s "/t" "/n" > OUTFILE.fasta
#awk
cat infile.fq | awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' > file.fa
#seqtk
seqtk seq -a input.fastq > output.fasta
#Bioawk
bioawk -c fastx '{print ">"$name"\n"$seq}' input.fastq > output.fasta
#Sed
sed -n '1~4s/^@/>/p;2~4p' INFILE.fastq > OUTFILE.fasta
