counting fastq(https://en.wikipedia.org/wiki/FASTQ_format) reads, bases, N Bases, Q20, Q30, GC with high performance
go install github.com/d2jvkpn/fastq_count$ 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:
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When input is -, read standard input;
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"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)
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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 |