Human Intestinal 16S rRNA gene reference taxonomy
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HITdb_v1.00
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README.md

README.md

HITdb - Human Intestinal 16S rRNA gene reference taxonomy

Ritari J, Salojärvi J, Lahti L & de Vos WM. Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database. BMC Genomics. 2015 Dec 12;16(1):1056. doi: 10.1186/s12864-015-2265-y.

Files

HITdb v1.00 contains HITdb 16S rRNA gene sequences in fasta format (HITdb_sequences.fna) and associated taxonomy text files in Qiime (HITdb_taxonomy_qiime.txt) and Mothur (HITdb_taxonomy_mothur.txt) formats.

Notes

  • HITdb is now integrated into the LotuS pipeline: http://psbweb05.psb.ugent.be/lotus

  • RDP or Mothur naïve Bayesian classifiers are recommended to be used with HITdb.

  • The HITdb taxonomy has six levels (Phylum, Class, Order, Family, Genus, Species) in order to make it compatible with Qiime analysis pipeline, in particular the summarize_taxa_through_plots.py script which outputs 6 levels of taxonomy.

  • Each OTU in HITdb has its nearest cultivable species determined based global sequence similarity. The "NN=" in OTU name indicates the nearest cultivable neighbour, and "D=" indicates the sequence similarity.

  • In Qiime, the following scripts can be employed to assign taxonomy to OTUs using HITdb with RDP as the assigner algorithm:

# taxonomy assignment
assign_taxonomy.py -i $PWD/otus/rep_set/seqs_rep_set.fasta -t $PWD/HITdb_taxonomy_qiime.txt -r $PWD/HITdb_sequences.fna -m rdp -o hitdb_taxonomy

# generating OTU table
make_otu_table.py -i $PWD/otus/uclust_picked_otus/seqs_otus.txt -t $PWD/hitdb_taxonomy/seqs_rep_set_tax_assignments.txt -o hitdb_otutable.biom

# output in tab and biom formats
summarize_taxa_through_plots.py -i hitdb_otutable.biom -m mapping.txt -o hitdb_taxa_summary

Version history

v. 1.00, 5 March 2015

First released version