microbiome__clinical__analysis临床微生物分析

1.NCBI RefSeq database基因组数据库
Kraken2：https://ccb.jhu.edu/software/kraken2/

2.NCBI nucleotide database基因数据库
dimond+MEGAN6:http://www.diamondsearch.org/index.php

3.Unique clade-specific marker genes进化标签基因
MetaPhlAn2:https://huttenhower.sph.harvard.edu/metaphlan

4.SURPI+一键化分析管道（临床推荐）

5.判断阈值
Viruses: non-overlapping reads from ≥3 distinct genomic regions
Bacteria, fungi, and parasites: a reads per million ratio minimum threshold ≥ 10

Miller S, Naccache S N, Samayoa E, et al. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid[J]. Genome research, 2019, 29(5): 831-842.

6.PRINSEQ去除测序数据中的重复片段:http://prinseq.sourceforge.net/

7.seqtk随机抽取1M的reads:https://github.com/lh3/seqtk
8.手动整理的病原微生物数据库:FDA­-ARGOS（https://www.ncbi.nlm.nih.gov/bioproject/231221）
Sichtig H et al., “FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science.”, Nat Commun, 2019 Jul 25;10(1):3313