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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



SILVA