Quick start¶

1. Install¶

cd gmeta
pixi install

2. Check the tool resolution¶

pixi run gmeta -V
pixi run gmeta db list     # shows kraken2/sylph database locations

3. Full pipeline from FASTQ¶

pixi run gmeta run sample_R1.fq.gz sample_R2.fq.gz \
  -s SAMPLE-001 \
  -D /data/db/kraken2 \
  --host-index /data/db/hg19 \
  -f json -f html -f xlsx -f pdf \
  -O gmeta-out/SAMPLE-001

Pipeline: fastp QC → bowtie2 host removal → kraken2 + bracken → reports in every selected format (<sample>.report.<fmt>), result JSON on stdout.

4. Report from existing results¶

Already ran kraken2 elsewhere? Skip the compute:

pixi run gmeta report -s SAMPLE-001 \
  --kreport kreport.txt --bracken bracken.txt --fastp-json fastp.json \
  -o SAMPLE-001.report.html        # format from extension

5. Surveillance submission workbook¶

pixi run gmeta net build kraken/*.report \
  --reads-dir raw_reads \
  --manifest ref_genome_manifest.csv \
  -o 识别网上报.xlsx --split-dir result/

混合样本 sheet: the template-exact eight columns (属/种中文名、序列数、相对丰度、种基因组覆盖度), 样本名称 only on each sample's first row.
审核明细 sheet: latin names, TaxID, accession, reference path, mean depth.
--split-dir: one single-sheet workbook per sample (sample id on every row).