d2jvkpn / fastq_count

fastq data reads, bases, N-bases, Q20, Q30, GC statistics

fastq_count

counting fastq(https://en.wikipedia.org/wiki/FASTQ_format) reads, bases, N Bases, Q20, Q30, GC with high performance

1. Installation

go install github.com/d2jvkpn/fastq_count

2. Usage

$ fastq_count [-phred value] [-output out.tsv] <input1.fastq input2.fastq.gz> output (tsv) header: Total reads Total bases N bases Q20 Q30 GC

Note:

• When input is -, read standard input;

• "pigz -dc *.fastq.gz | fastq_count -" is recommended for gzipped file(s).

  -output string: output summary to a tsv file, default: stdout

  -phred int: set phred value (default 33)

• output example (tsv):

Reads	Bases	N-bases	GC	Q20	Q30
1.00 M	0.15 G	0.00%	44.20%	96.69%	91.59%
1000000	150000000	5099	66294072	145037238	137378352