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FASTQ to FASTA

  • Public
By Jit 1054 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