statistics #

FASTA/FASTQ base count: #

• FASTA with awk (usually preinstalled):

  1awk 'NF && !/^>/ {total += length} END {print total}' *fasta
  

• You can specify one or more files. The sum of all bases from all files together will be the output.
• FASTA/FASTQ with seqtk, parallel and awk:

   1parallel seqtk size ::: *.fasta | awk -F'\t' '{sum+=$2;} END{print sum;}'
   2
   3# or
   4parallel seqtk size ::: *.fastq | awk -F'\t' '{sum+=$2;} END{print sum;}'
   5
   6# without awk
   7parallel seqtk size ::: *.fastq # This prints no. of reads and base count per file
   8
   9# for just one file without parallel:
  10seqtk size file.fastq