Usage¶
Three command families share the same parsers and report model:
| Command | Input | Output |
|---|---|---|
gmeta run |
FASTQ | pipeline: QC → host removal → profiling → reports |
gmeta report |
profiler result files | JSON/HTML/Excel/PDF report |
gmeta net build |
profiler result files | 识别网 submission workbook |
Method matrix¶
All six profilers are both executable (gmeta run -m <method>) and
importable (gmeta report / gmeta net build):
| Method | Execute | Import formats |
|---|---|---|
| kraken2 + bracken | ✅ | kreport, bracken table |
| sylph | ✅ | profile TSV |
| centrifuge | ✅ | native report, kreport (via centrifuge-kreport) |
| kaiju | ✅ | kaiju2table (species + genus) |
| metaphlan | ✅ | profile (rel_ab / rel_ab_w_read_stats) |
| kmcp | ✅ | compute profile TSV (17 columns) |
Where to go¶
- CLI reference — every flag of run/report/db
- 识别网 export — submission workbook deep-dive
- Supported profilers — input formats and semantics per tool
- Coverage — how 种基因组覆盖度 is computed