12.8 宏基因组物种分类原理
当前使用的宏基因组物种分类方法，主要是使用NCBI的物种分类数据库进行分类。将测序数据与NCBI的序列数据库经行比对，例如nt库，nr库，refseq数据库等。如果测序数据与数据库中序列具有很好的相似性，而认为二者为同源序列，具有相同的祖先。将测序ID转换为NCBI Accession ID，然后将Accession ID转换为物种分类Tax ID。则得到了测序数据的物种分类信息。物种分类本质上则是根据序列相似性进行三种ID相互转换的过程。
图 1 利用纳米孔测序进行快速鉴定示意图
**测序序列ID：**标记每条测序数据，每条序列的ID不同，不同测序平台采用不同的表示方法，fastq文件中第一行@符号行，没有特殊意义。
**Accession ID：**A unique alphanumeric character string that is used to unambiguously identify a particular record in a database. Examples include MGI accession IDs, GenBank accession IDs, and PubMed accession IDs.
表 1 NCBI Accession Number
| Accession prefix | Molecule type | Comment |
|---|---|---|
| AC_ | Genomic | Complete genomic molecule, usually alternate assembly |
| NC_ | Genomic | Complete genomic molecule, usually reference assembly |
| NG_ | Genomic | Incomplete genomic region |
| NT_ | Genomic | Contig or scaffold, clone-based or WGSa |
| NW_ | Genomic | Contig or scaffold, primarily WGSa |
| NZ_b | Genomic | Complete genomes and unfinished WGS data |
| NM_ | mRNA | Protein-coding transcripts (usually curated) |
| NR_ | RNA | Non-protein-coding transcripts |
| XM_c | mRNA | Predicted model protein-coding transcript |
| XR_c | RNA | Predicted model non-protein-coding transcript |
| AP_ | Protein | Annotated on AC_ alternate assembly |
| NP_ | Protein | Associated with an NM_ or NC_ accession |
| YP_c | Protein | Annotated on genomic molecules without an instantiated transcript record |
| XP_c | Protein | Predicted model, associated with an XM_ accession |
| WP_ | Protein | Non-redundant across multiple strains and species |
**Taxon ID：**This is shared by all names for a specific TaxNode. Each TaxNode has a stable, unique numerical identifier, the taxonomy identifier (TaxId). Each TaxId has a labelled primary name (a formal or informal name) which shows up on the NCBI records.
In publications this can be standardized as a primary name with its TaxId displayed as “NCBI:txid” followed by a number, e.g.
Homo sapiens NCBI:txid9606
表 1 NCBI物种分类数据库统计
https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=STATISTICS&uncultured=hide&unspecified=hide
**三者之间的关系：**测序的ID可以比对到多个Accession ID，序列越长，唯一性越好，选择比对最好的Accession ID。由于物种分类包括过个层级，一个Accession对应唯一Taxon ID。一个Taxon ID中可以包含多个Accession ID。每个Taxon还对应一个parent taxid，对应一个division id。
举列：
有一条序列，比对到了Accession ID是NC_000001，NC_000001对应的Taxon ID为9606。9606对应的name为Homo sapiens，9606的parent tax_id为9605，对应Homo。对应的division id为5，Primates灵长类。
@ERR4007992.1 NB501556:135:HTCW3AFXY:1:11101:9571:1066 length=76
AATTTGACCAGAAGTTATGGGCATCCCTCCCCTGGGAAGGAGGCAGGCAGAAAAGTTTGGAATCTATGTAGTAAAA
+
AAA/A/6//EE/EEEEEEEE/EEE/<E/EEEAE/EEE6EE//E/6EE/EE/E/E/AEE6/EE/E//E//6//E</E