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File formats

Inputs gmeta parses

kraken2 kreport (tab-separated, no header)

100.00  100000  0     R  1    root
 40.00  40000   40000 S  9606   Homo sapiens
 30.00  29500   500   G  641     Vibrio
 25.00  25000   25000 S  662       Vibrio cholerae

Columns: percent | clade reads (children included) | direct reads | rank code | taxid | indented name. The name indentation is the tree — species pair with their nearest genus ancestor by indent depth. R/U rows supply classified/unclassified totals. Space-aligned reports and taxid-less variants are also accepted.

bracken

Header name tax_id taxonomy_lvl kraken_assigned_reads added_reads new_est_reads fraction_total_reads; species rows (S) only. The fraction column is a percentage (sums ~100); scale is auto-detected so 0..1 inputs also parse.

centrifuge native report

name taxID taxRank genomeSize numReads numUniqueReads abundance, no header. taxRank species/genus rows feed the 识别网 adapter; the abundance column (0..1) wins over reads-based recomputation.

kaiju2table

Header file percent reads taxon_id taxon_name; taxon_name may be a "; "-joined lineage. Generate with -l species (and -l genus for the genus table).

MetaPhlAn profile

#clade_name NCBI_tax_id relative_abundance [additional_species] rows (g__… genus, s__… species). rel_ab_w_read_stats adds estimated_number_of_reads_from_the_clade, parsed by header name.

KMCP profile (17 columns)

ref percentage coverage score chunksFrac chunksRelDepth chunksRelDepthStd reads ureads hicureads refsize refname taxid rank taxname taxpath taxpathsn. Requires taxid (+taxname or refname); per-reference rows are aggregated by taxid.

sylph profile

Header includes Genome_file, Adjusted_ANI, Eff_cov, Taxonomic_abundance.

Outputs gmeta writes

识别网 workbook (xlsx)

Sheet 混合样本: 样本名称 | 属中文名 | 属序列数 | 属相对丰度 | 种中文名 | 种序列数 | 种基因组覆盖度 | 种相对丰度 — abundances as 48.23% strings, coverage as 0–100 floats, 样本名称 only on each sample's first row. Sheet 审核明细: 样本名称 | 属拉丁名 | 属中文名 | 种拉丁名 | 种中文名 | TaxID | 属序列数 | 种序列数 | 种相对丰度 | accession | 参考基因组 | 参考基因组长度 | 平均测序深度 | 覆盖度1x(%).

Report files

.json — MetaReport. .html — self-contained Jinja2 template. .xlsx — 检测概览 + 物种检出 sheets. .pdf — WeasyPrint render of the HTML template.

fetch scripts (db fetch)

One fetch-<tool>.sh per target: set -euo pipefail, resumable download helper, install under $GMETA_DB_DIR, layout verification, plus run_all.sh.