物种注释

最后发布时间 : 2022-11-04 12:59:03 浏览量 :

RDP物种注释(rdp_16s_v18)更快，但缺少完整真核来源数据,可能不完整，耗时15s;
SILVA数据库(silva_16s_v123.fa)更好注释真核、质体序列，极慢耗时3h起
置信阈值通常0.6/0.8，vserch最低0.1/usearch可选0输出最相似物种注释用于观察潜在分类

otus.fa

>ASV_1
GTAGTCCACGCCGTAAACGGTGGGCGCTAGATGTGGGGACCTTCCACGGTTTCTGCGTCGCAGCTAACGCATTAAGCGCC
CCGCCTGGGGAGTACGGTCGCAAGACTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAGCATGTTGCTTA
ATTCGACGCAACGCGAAGAACCTTACCAAGGCTTGACATCGCCGGAAAACTCGCAGAGATGCGGGGTCCTTTTGGGCCGG
TGACAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCGTTCT
ATGTTGCCAGCACGCCCTTCGGGGTGGTGGGGACTCATAGGAGACTGCCGGGGTCAACTCGGA
>ASV_2
GTAGTCCACGCCCTAAACGATGTCAACTGGTTGTTGGGAGGGTTTCTTCTCAGTAACGTAGCTAACGCGTGAAGTTGACC
GCCTGGGGAGTACGGCCGCAAGGTTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTGGTTTAAT
TCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGTCTGGAATCCTGAAGAGATTTGGGAGTGCTCGAAAGAGAGCC
AGAACACAGGTGCTGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGT
CATTAGTTGCTACGAAAGGGCACTCTAATGAGACTGCCGGTGACAAACCGGA

rdp_16s_v18.fa

>AJ000684;tax=d:Bacteria,p:Actinobacteria,c:Actinobacteria,o:Mycobacteriales,f:Mycobacteriaceae,g:Mycobacterium;
GAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGGAAAGGTCTCTTCGGAGATACTCGAGTGGCGAACGGGTGAGT
AACACGTGGGTAATCTGCCCTGCACATCGGGATAAGCCTGGGAAACTGGGTCTAATACCGAATAGGACCTCGAGGCGCAT
GCCTTGTGGTGGAAAGCTTTTGCGGTGTGGGATGGGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGACGGCCTACCAAGG
CGACGACGGGTAGCCGGCCTGAGAGGGTGTCCGGCCACACTGGGACTGAGATACGGCCCAGACTCCTACGGGAGGCAGCA
GTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCGACGCCGCGTGGGGGATGACGGNCTTCGGGTTGTAAACCTC
TTTCAGCAGGGACGAAGCGCAAGTGACGGTACCTGCAGAAGAAGCACCGGCCAACTACGTGCCAGCAGCCGCGGTAATAC
GTAGGGTGCGAGCGTTGTCCGGAATTACTGGGCGTAAAGAGCTCGTAGGTGGTTTGTCGCGTTGTTCGTGAAAACCGGGG
GCTTAACCCTCGGCGTGCGGGCGATACGGGCAGACTGGAGTACTGCAGGGGAGACTGGAATTCCTGGTGTAGCGGTGGAA
TGCGCAGATATCAGGAGGAACACCGGTGGCGAAGGCGGGTCTCTGGGCAGTAACTGACGCTGAGGAGCGAAAGCGTGGGG
AGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGGTGGGTACTAGGTGTGGGTTTCCTTCCTTGGGATCCGT
GCCGTAGCTAACGCATTAAGTACCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGC
ACAAGCGGCGGAGCATGTGGATTAATTCGATGCAACGCGAAGAACCTTACCTGGGTTTGACATGCACAGGACGCCGGCAG
AGATGTCGGTTCCCTTGTGGCCTGTGTGCAGGTGGTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTC
CCGCAACGAGCGCAACCCTTGTCTCATGTTGCCAGCGGGTAATGCCGGGGACTCGTGAGAGACTGCCGGGGTCAACTCGG
AGGAAGGTGGGGATGACGTCAAGTCATCATGCCCCTTATGTCCAGGGCTTCACACATGCTACAATGGCCGGTACAAAGGG
CTGCGATGCCGCAAGGTTAAGCGAATCCTTTTAAAGCCGGTCTCAGTTCGGATCGGGGTCTGCAACTCGACCCCGTGAAG
TCGGAGTCGCTAGTAATCGCAGATCAGCAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCA
TGAAAGTCGGTAACACCCGAAGCCAGTGGCCTAACCTTTGGGAGGGAGCTGTCGAAGGTGGGATCGGCGATTGGGACGAA
GTCGT

vsearch --sintax results/raw/otus.fa \
    --db data/db/usearch/rdp_16s_v18.fa \
    --sintax_cutoff 0.1 \
    --tabbedout results/matrix/otus.sintax 

sed -i 's/\r//' results/raw/otus.sintax

otus.sintax

ASV_13	d:Bacteria(1.00),p:Bacteroidetes(1.00),c:Flavobacteriia(1.00),o:Flavobacteriales(1.00),f:Flavobacteriaceae(1.00),g:Flavobacterium(1.00)	+	d:Bacteria,p:Bacteroidetes,c:Flavobacteriia,o:Flavobacteriales,f:Flavobacteriaceae,g:Flavobacterium
ASV_17	d:Bacteria(1.00),p:Proteobacteria(1.00),c:Betaproteobacteria(1.00),o:Burkholderiales(1.00),f:Comamonadaceae(1.00),g:Piscinibacter(0.32)	+	d:Bacteria,p:Proteobacteria,c:Betaproteobacteria,o:Burkholderiales,f:Comamonadaceae,g:Piscinibacter
ASV_7	d:Bacteria(1.00),p:Bacteroidetes(1.00),c:Flavobacteriia(1.00),o:Flavobacteriales(1.00),f:Flavobacteriaceae(1.00),g:Flavobacterium(1.00)	+	d:Bacteria,p:Bacteroidetes,c:Flavobacteriia,o:Flavobacteriales,f:Flavobacteriaceae,g:Flavobacterium
ASV_5	d:Bacteria(1.00),p:Cyanobacteria/Chloroplast(1.00),c:Chloroplast(1.00),f:Chloroplast(1.00),g:Streptophyta(1.00)	+	d:Bacteria,p:Cyanobacteria/Chloroplast,c:Chloroplast,f:Chloroplast,g:Streptophyta
ASV_1	d:Bacteria(1.00),p:Actinobacteria(1.00),c:Actinobacteria(1.00),o:Streptosporangiales(0.85),f:Thermomonosporaceae(0.80),g:Actinocorallia(0.48)	+	d:Bacteria,p:Actinobacteria,c:Actinobacteria,o:Streptosporangiales,f:Thermomonosporaceae,g:Actinocorallia
ASV_2	d:Bacteria(1.00),p:Proteobacteria(1.00),c:Betaproteobacteria(1.00),o:Burkholderiales(1.00),f:Comamonadaceae(1.00),g:Pelomonas(1.00)	+	d:Bacteria,p:Proteobacteria,c:Betaproteobacteria,o:Burkholderiales,f:Comamonadaceae,g:Pelomonas
ASV_3	d:Bacteria(1.00),p:Proteobacteria(1.00),c:Betaproteobacteria(1.00),o:Burkholderiales(1.00),f:Comamonadaceae(1.00),g:Rhizobacter(0.92)	+	d:Bacteria,p:Proteobacteria,c:Betaproteobacteria,o:Burkholderiales,f:Comamonadaceae,g:Rhizobacter

特征表构建去除质体和非细菌