- python3
- Qiime
- click - pip install click
- usearch6.x version
- cutadapt
- krona
How to install required tools
conda install above tools -y -c bioconda
Fastq file names shouldn't be modified.
==> 16s_params.txt <==
pick_otus:enable_rev_strand_match True
assign_taxonomy:id_to_taxonomy_fp gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
assign_taxonomy:reference_seqs_fp gg_13_8_otus/rep_set/97_otus.fasta
==> 16s_div.txt <==
alpha_diversity:metrics shannon,simpson,observed_otus,PD_whole_tree,chao1
beta_diversity:metrics unweighted_unifrac,weighted_unifrac
==> its_params.txt <==
pick_otus:enable_rev_strand_match True
assign_taxonomy:assignment_method blast
assign_taxonomy:id_to_taxonomy_fp its_unite/sh_taxonomy_qiime_ver7_dynamic_20.11.2016.txt
assign_taxonomy:reference_seqs_fp its_unite/sh_refs_qiime_ver7_dynamic_20.11.2016.fasta
As you probably downloaded the database, set those files paths to a database_info.json.
To run preprocess and otu clustering
python3 preprocess.py --help
To run diversity analysis
python3 postprocess.py --help
To generate upgma dendrogram
upgma_cluster.py -i *dm.txt -o *.tre
- "THE BEER-WARE LICENSE" (Revision 42):
- [email protected] wrote this file. As long as you retain this notice you
- can do whatever you want with this stuff. If we meet some day, and you think
- this stuff is worth it, you can buy me a beer in return jkkim