从基因组直接建树,de_novo_wf:构建新树并用GTDB注释,包括鉴定、比对、推断树、确定根和装饰。 输入文件为细菌基因组的目录(—genome_dir),指定扩展名类型(—extension),以及输出目录(—out_dir)。必须参数有需要选择细菌(—bacteria)/古菌,指定外类群(—outgroup_taxon)。可选常用参数有结果前缀(—prefix)和使用...
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> gtdbtk de_novo_wf --genome_dir ./genomes --bac120_ms --outgroup_taxon p__Chloroflexota --taxa_filter p__Firmicutes --out_dir de_novo_output Individual stepsAll steps comprising the classify and de novo workflows can be run independently if desired. Please consult the command line ...