1. Daisuke Motooka Avatar Daisuke Motooka
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ntF-ITS1 database

High-throughput sequencing of Internal Transcribed Spacer (ITS) is the de facto standard for fungal metagenomics. The ntF-ITS1 (nt-Fungi ITS1) database is curated ITS1 database which was utilized to taxonomic assignment of fungal community. This ntF-ITS1 supports QIIME pipeline.

How to use

For QIIME1

1.Download and unzip

URL : https://bitbucket.org/daisukem/fungi/downloads

#!shell script

wget https://bitbucket.org/daisukem/fungi/downloads/ntF-ITS1_2018.zip
unzip ntF-ITS1_2018.zip
you can find two files (text and fasta format). The text file includes assigned taxonomy which supports QIIME pipeline. The fasta file is reference sequences. For RDP, this is used as training sequences for the classifier.

2.Clustering, taxonomic assignment and summarization using QIIME pipeline

Inputs files are

  1. Sequence file with fasta format (seqs.fasta)
  2. ntF-ITS1 database files
  3. sample information file (samples.txt)

<Picking OTUs with 95% sequence similarity> 

#!python
pick_otus.py -i seqs.fasta -o otus -s 0.95

<Picking a representative sequence for each OTU> 

#!python
pick_rep_set.py -i otus/seqs_otus.txt -f seqs.fasta -o otus/rep_set.fasta

<Taxonomic assignment for each OTU> 

#!python
assign_taxonomy.py -i otus/rep_set.fasta -o otus/rdp_assign_taxonomy -t ntF-ITS1.txt -r ntF-ITS1.fasta -m rdp --rdp_max_memory 10000 -c 0.55

<Making OTU table> 

#!python
make_otu_table.py -i otus/seqs_otus.txt -t otus/rdp_assign_taxonomy/rep_set_tax_assignments.txt -o otus/otu_table.biom

<Summarizing and Plotting taxonomic summary> 

#!python
summarize_taxa_through_plots.py -i otus/otu_table.biom -o wf_taxa_summary -m samples.txt -s

Cite ntF-ITS1

Motooka D. et al., Frontiers in Microbiology, 2017, doi: 10.3389/fmicb.2017.00238

Updated