Greengenes

QIIME1 - location of greengenes database

# to find the version and location of the greengenes reference database, look to the qiime1 default settings:

print_qiime_config.py -t

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pick_otus_reference_seqs_fp: .miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

sc_queue: all.q

topiaryexplorer_project_dir: None

pynast_template_alignment_fp: .miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta

cluster_jobs_fp: start_parallel_jobs.py

pynast_template_alignment_blastdb: None

assign_taxonomy_reference_seqs_fp: .miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

torque_queue: friendlyq

jobs_to_start: 1

slurm_time: None

denoiser_min_per_core: 50

assign_taxonomy_id_to_taxonomy_fp: .miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt

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# Location: in this example the greengenes database files are located at:

.miniconda2/envs/qiime1/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/

__init__.py

__init__.pyc

rep_set/97_otus.fasta

rep_set_aligned/85_otus.pynast.fasta

taxonomy/97_otu_taxonomy.txt

trees/97_otus.tree

Greengenes versions

http://greengenes.secondgenome.com/downloads

SILVA

→ How to replace Greengenes (QIIME1 default) with SILVA reference database?