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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
2.Clustering, taxonomic assignment and summarization using QIIME pipeline
Inputs files are
- Sequence file with fasta format (seqs.fasta)
- ntF-ITS1 database files
- 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