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add_taxa
add_taxa
 
 
adjust_seq_orientation
adjust_seq_orientation
 
 
alpha_diversity
alpha_diversity
 
 
alpha_rarefaction
alpha_rarefaction
 
 
beta_diversity
beta_diversity
 
 
beta_diversity_through_plots
beta_diversity_through_plots
 
 
beta_significance
beta_significance
 
 
compare_taxa_summaries
compare_taxa_summaries
 
 
compute_core_microbiome
compute_core_microbiome
 
 
conditional_uncovered_probability
conditional_uncovered_probability
 
 
convert_otu_table_to_unifrac_sample_mapping
convert_otu_table_to_unifrac_sample_mapping
 
 
convert_unifrac_sample_mapping_to_otu_table
convert_unifrac_sample_mapping_to_otu_table
 
 
core_qiime_analyses
core_qiime_analyses
 
 
filter_fasta
filter_fasta
 
 
filter_otus_from_otu_table
filter_otus_from_otu_table
 
 
filter_samples_from_otu_table
filter_samples_from_otu_table
 
 
jackknifed_beta_diversity
jackknifed_beta_diversity
 
 
make_distance_boxplots
make_distance_boxplots
 
 
make_distance_comparison_plots
make_distance_comparison_plots
 
 
make_otu_heatmap_html
make_otu_heatmap_html
 
 
make_otu_network
make_otu_network
 
 
make_otu_table
make_otu_table
 
 
make_tep
make_tep
 
 
map_reads_to_reference
map_reads_to_reference
 
 
merge_otu_tables
merge_otu_tables
 
 
multiple_rarefactions
multiple_rarefactions
 
 
multiple_rarefactions_even_depth
multiple_rarefactions_even_depth
 
 
otu_category_significance
otu_category_significance
 
 
parallel_align_seqs_pynast
parallel_align_seqs_pynast
 
 
parallel_alpha_diversity
parallel_alpha_diversity
 
 
parallel_assign_taxonomy_blast
parallel_assign_taxonomy_blast
 
 
parallel_assign_taxonomy_rdp
parallel_assign_taxonomy_rdp
 
 
parallel_beta_diversity
parallel_beta_diversity
 
 
parallel_blast
parallel_blast
 
 
parallel_identify_chimeric_seqs
parallel_identify_chimeric_seqs
 
 
parallel_map_reads_to_reference
parallel_map_reads_to_reference
 
 
parallel_multiple_rarefactions
parallel_multiple_rarefactions
 
 
parallel_pick_otus_blast
parallel_pick_otus_blast
 
 
parallel_pick_otus_trie
parallel_pick_otus_trie
 
 
parallel_pick_otus_uclust_ref
parallel_pick_otus_uclust_ref
 
 
per_library_stats
per_library_stats
 
 
pick_otus_through_otu_table
pick_otus_through_otu_table
 
 
pick_reference_otus_through_otu_table
pick_reference_otus_through_otu_table
 
 
pick_subsampled_reference_otus_through_otu_table
pick_subsampled_reference_otus_through_otu_table
 
 
plot_rank_abundance_graph
plot_rank_abundance_graph
 
 
shared_phylotypes
shared_phylotypes
 
 
simsam
simsam
 
 
single_rarefaction
single_rarefaction
 
 
sort_otu_table
sort_otu_table
 
 
split_libraries_fastq
split_libraries_fastq
 
 
split_otu_table
split_otu_table
 
 
split_otu_table_by_taxonomy
split_otu_table_by_taxonomy
 
 
start_parallel_jobs
start_parallel_jobs
 
 
summarize_otu_by_cat
summarize_otu_by_cat
 
 
summarize_taxa
summarize_taxa
 
 
summarize_taxa_through_plots
summarize_taxa_through_plots
 
 
supervised_learning
supervised_learning
 
 
transform_coordinate_matrices
transform_coordinate_matrices
 
 
trflp_file_to_otu_table
trflp_file_to_otu_table
 
 
README.md
README.md
 
 
script_usage_tests.py
script_usage_tests.py
 
 

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qiime_test_data

Test input and output for QIIME scripts.

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Test input and output for QIIME scripts.

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  • JavaScript 90.1%
  • Perl 5.1%
  • Shell 4.6%
  • Python 0.2%