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ftp_contents.txt
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ftp_contents.txt
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ftp://ftp.microbio.me/emp/release1/
README
about_mapping_files.md
about_otu_tables.pdf
emp_ontology/empo_v3.csv
emp_ontology/envoEmpo_graph_v3.vue
mapping_files/emp_qiime_mapping_release1.tsv mapping_files/emp_qiime_mapping_subset_5k.tsv
mapping_files/emp_qiime_mapping_qc_filtered.tsv mapping_files/emp_qiime_mapping_subset_10k.tsv
mapping_files/emp_qiime_mapping_subset_2k.tsv
otu_distributions/otu_summary.emp_deblur_90bp.subset_2k.rare_5000.tsv
otu_distributions/otu_summary_no_chl.emp_deblur_90bp.subset_2k.rare_5000.tsv
otu_distributions/emp_2k_subset_blank_stats.tsv
otu_info/deblur:
emp.90.min25.deblur.seq.fa emp90.5000_1000_rxbl_placement_pruned75.tog.tre
emp.100.min25.deblur.seq.fa emp100.5000_1000_rxbl_placement_pruned75.tog.tre
emp.150.min25.deblur.seq.fa emp150.5000_1000_rxbl_placement_pruned75.tog.tre
otu_info/greengenes_13_8:
97_otu_map.txt 97_otus.fasta 97_otus_aligned.fasta
97_otu_taxonomy.txt 97_otus.tree 97_otus_unannotated.tree
otu_info/greengenes_sepp_pipeline:
sepp-package.zip
otu_info/open_ref:
rep_set.fna (excludes sample singletons) rep_set.incl_sample_singletons.fna
rep_set.tre (excludes sample singletons)
otu_info/silva_123:
97_otus.tre Silva_123_notes.txt taxonomy/
97_otus_16S.fasta core_alignment_SILVA123.fasta
otu_tables/closed_ref_greengenes:
(unfiltered tables:)
emp_cr_gg_13_8.release1.biom
emp_cr_gg_13_8.release1.summary.txt
(subsets:)
emp_cr_gg_13_8.qc_filtered.biom emp_cr_gg_13_8.subset_2k.biom
emp_cr_gg_13_8.qc_filtered.rare_10000.biom emp_cr_gg_13_8.subset_2k.rare_10000.biom
emp_cr_gg_13_8.qc_filtered.rare_10000.summary.txt emp_cr_gg_13_8.subset_2k.rare_10000.summary.txt
emp_cr_gg_13_8.qc_filtered.summary.txt emp_cr_gg_13_8.subset_2k.summary.txt
emp_cr_gg_13_8.subset_10k.biom emp_cr_gg_13_8.subset_5k.biom
emp_cr_gg_13_8.subset_10k.rare_10000.biom emp_cr_gg_13_8.subset_5k.rare_10000.biom
emp_cr_gg_13_8.subset_10k.rare_10000.summary.txt emp_cr_gg_13_8.subset_5k.rare_10000.summary.txt
emp_cr_gg_13_8.subset_10k.summary.txt emp_cr_gg_13_8.subset_5k.summary.txt
otu_tables/closed_ref_silva:
(unfiltered tables:)
emp_cr_silva_16S_123.release1.biom
emp_cr_silva_16S_123.release1.summary.txt
(subsets:)
emp_cr_silva_16S_123.qc_filtered.biom emp_cr_silva_16S_123.subset_2k.biom
emp_cr_silva_16S_123.qc_filtered.rare_10000.biom emp_cr_silva_16S_123.subset_2k.rare_10000.biom
emp_cr_silva_16S_123.qc_filtered.rare_10000.summary.txt emp_cr_silva_16S_123.subset_2k.rare_10000.summary.txt
emp_cr_silva_16S_123.qc_filtered.summary.txt emp_cr_silva_16S_123.subset_2k.summary.txt
emp_cr_silva_16S_123.subset_10k.biom emp_cr_silva_16S_123.subset_5k.biom
emp_cr_silva_16S_123.subset_10k.rare_10000.biom emp_cr_silva_16S_123.subset_5k.rare_10000.biom
emp_cr_silva_16S_123.subset_10k.rare_10000.summary.txt emp_cr_silva_16S_123.subset_5k.rare_10000.summary.txt
emp_cr_silva_16S_123.subset_10k.summary.txt emp_cr_silva_16S_123.subset_5k.summary.txt
otu_tables/deblur:
(unfiltered tables:)
emp_deblur_90bp.release1.biom
emp_deblur_90bp.release1.summary.txt
emp_deblur_100bp.release1.biom
emp_deblur_100bp.release1.summary.txt
emp_deblur_150bp.release1.biom
emp_deblur_150bp.release1.summary.txt
(subsets:)
emp_deblur_100bp.qc_filtered.biom emp_deblur_150bp.subset_2k.biom
emp_deblur_100bp.qc_filtered.rare_5000.biom emp_deblur_150bp.subset_2k.rare_5000.biom
emp_deblur_100bp.qc_filtered.rare_5000.summary.txt emp_deblur_150bp.subset_2k.rare_5000.summary.txt
emp_deblur_100bp.qc_filtered.summary.txt emp_deblur_150bp.subset_2k.summary.txt
emp_deblur_100bp.subset_10k.biom emp_deblur_150bp.subset_5k.biom
emp_deblur_100bp.subset_10k.rare_5000.biom emp_deblur_150bp.subset_5k.rare_5000.biom
emp_deblur_100bp.subset_10k.rare_5000.summary.txt emp_deblur_150bp.subset_5k.rare_5000.summary.txt
emp_deblur_100bp.subset_10k.summary.txt emp_deblur_150bp.subset_5k.summary.txt
emp_deblur_100bp.subset_2k.biom emp_deblur_90bp.qc_filtered.biom
emp_deblur_100bp.subset_2k.rare_5000.biom emp_deblur_90bp.qc_filtered.rare_5000.biom
emp_deblur_100bp.subset_2k.rare_5000.summary.txt emp_deblur_90bp.qc_filtered.rare_5000.summary.txt
emp_deblur_100bp.subset_2k.summary.txt emp_deblur_90bp.qc_filtered.summary.txt
emp_deblur_100bp.subset_5k.biom emp_deblur_90bp.subset_10k.biom
emp_deblur_100bp.subset_5k.rare_5000.biom emp_deblur_90bp.subset_10k.rare_5000.biom
emp_deblur_100bp.subset_5k.rare_5000.summary.txt emp_deblur_90bp.subset_10k.rare_5000.summary.txt
emp_deblur_100bp.subset_5k.summary.txt emp_deblur_90bp.subset_10k.summary.txt
emp_deblur_150bp.qc_filtered.biom emp_deblur_90bp.subset_2k.biom
emp_deblur_150bp.qc_filtered.rare_5000.biom emp_deblur_90bp.subset_2k.rare_5000.biom
emp_deblur_150bp.qc_filtered.rare_5000.summary.txt emp_deblur_90bp.subset_2k.rare_5000.summary.txt
emp_deblur_150bp.qc_filtered.summary.txt emp_deblur_90bp.subset_2k.summary.txt
emp_deblur_150bp.subset_10k.biom emp_deblur_90bp.subset_5k.biom
emp_deblur_150bp.subset_10k.rare_5000.biom emp_deblur_90bp.subset_5k.rare_5000.biom
emp_deblur_150bp.subset_10k.rare_5000.summary.txt emp_deblur_90bp.subset_5k.rare_5000.summary.txt
emp_deblur_150bp.subset_10k.summary.txt emp_deblur_90bp.subset_5k.summary.txt
otu_tables/open_ref_greengenes:
(unfiltered tables:)
emp_or_gg_13_8.release1.biom (excludes sample singletons) emp_or_gg_13_8.release1.summary.txt
emp_or_gg_13_8.incl_sample_singletons.biom emp_or_gg_13_8.incl_sample_singletons.summary.txt
(subsets: can be generated manually using QIIME)
otu_tables/picrust:
README_PICRUSt.txt emp_cr_gg_13_8.normalized.biom nsti_per_sample.tsv
cog_predictions.biom ko_predictions.biom rfam_predictions.biom
results/alpha_diversity/deblur/emp.90:
emp.90.min25.deblur.withtax.onlytree_1000.txt emp.90.min25.deblur.withtax.onlytree_30000.txt
emp.90.min25.deblur.withtax.onlytree_10000.txt emp.90.min25.deblur.withtax.onlytree_5000.txt
emp.90.min25.deblur.withtax.onlytree_100000.txt
results/alpha_diversity/deblur/emp.100:
emp.100.min25.deblur.withtax.onlytree_1000.txt emp.100.min25.deblur.withtax.onlytree_30000.txt
emp.100.min25.deblur.withtax.onlytree_10000.txt emp.100.min25.deblur.withtax.onlytree_5000.txt
emp.100.min25.deblur.withtax.onlytree_100000.txt
results/alpha_diversity/deblur/emp.150:
emp.150.min25.deblur.withtax.onlytree_1000.txt emp.150.min25.deblur.withtax.onlytree_30000.txt
emp.150.min25.deblur.withtax.onlytree_10000.txt emp.150.min25.deblur.withtax.onlytree_5000.txt
emp.150.min25.deblur.withtax.onlytree_100000.txt
results/beta_diversity/deblur:
emp_deblur_unifrac_dist.tar.gz emp_90_gg_1k_unweighted_unifrac.txt.gz
emp_deblur_unifrac_pc.tar.gz emp_150_gg_1k_unweighted_unifrac.txt.gz
emp_deblur_unifrac_emperor.tar.gz