Seqstats is a small tool written in C on top of the excellent klib library by Heng Li. It provides general summary statistics of both read and assembly files. It can read fastq and fasta files, either gzipped or plain.

git clone --recursive https://github.com/clwgg/seqstats

cd seqstats
make

You can directly supply seqstats with (gzipped) fasta and fastq files. If you want to input multiple files, cat-pipe them into seqstats and use “-” to symbolize to seqstats to read from STDIN.

seqstats infile.fasta
seqstats infile.fa.gz

seqstats infile.fastq
seqstats infile.fq.gz

cat in1.fq.gz in2.fq.gz > seqstats -
cat chr*.fa > seqstats -