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 |