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add_qiime_labels
add_qiime_labels
 
 
add_taxa
add_taxa
 
 
adjust_seq_orientation
adjust_seq_orientation
 
 
align_seqs
align_seqs
 
 
alpha_diversity
alpha_diversity
 
 
alpha_rarefaction
alpha_rarefaction
 
 
assign_taxonomy
assign_taxonomy
 
 
beta_diversity
beta_diversity
 
 
beta_diversity_through_plots
beta_diversity_through_plots
 
 
beta_significance
beta_significance
 
 
blast_wrapper
blast_wrapper
 
 
check_id_map
check_id_map
 
 
cluster_quality
cluster_quality
 
 
collate_alpha
collate_alpha
 
 
compare_3d_plots
compare_3d_plots
 
 
compare_alpha_diversity
compare_alpha_diversity
 
 
compare_categories
compare_categories
 
 
compare_distance_matrices
compare_distance_matrices
 
 
compare_taxa_summaries
compare_taxa_summaries
 
 
compute_core_microbiome
compute_core_microbiome
 
 
conditional_uncovered_probability
conditional_uncovered_probability
 
 
consensus_tree
consensus_tree
 
 
convert_fastaqual_fastq
convert_fastaqual_fastq
 
 
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
 
 
count_seqs
count_seqs
 
 
demultiplex_fasta
demultiplex_fasta
 
 
denoiser_preprocess
denoiser_preprocess
 
 
dissimilarity_mtx_stats
dissimilarity_mtx_stats
 
 
distance_matrix_from_mapping
distance_matrix_from_mapping
 
 
extract_seqs_by_sample_id
extract_seqs_by_sample_id
 
 
filter_alignment
filter_alignment
 
 
filter_distance_matrix
filter_distance_matrix
 
 
filter_fasta
filter_fasta
 
 
filter_otus_by_sample
filter_otus_by_sample
 
 
filter_otus_from_otu_table
filter_otus_from_otu_table
 
 
filter_samples_from_otu_table
filter_samples_from_otu_table
 
 
filter_tree
filter_tree
 
 
identify_missing_files/ALIGN_BQ7_
identify_missing_files/ALIGN_BQ7_
 
 
inflate_denoiser_output
inflate_denoiser_output
 
 
jackknifed_beta_diversity
jackknifed_beta_diversity
 
 
make_2d_plots
make_2d_plots
 
 
make_3d_plots
make_3d_plots
 
 
make_distance_boxplots
make_distance_boxplots
 
 
make_distance_comparison_plots
make_distance_comparison_plots
 
 
make_distance_histograms
make_distance_histograms
 
 
make_fastq
make_fastq
 
 
make_otu_heatmap_html
make_otu_heatmap_html
 
 
make_otu_network
make_otu_network
 
 
make_otu_table
make_otu_table
 
 
make_phylogeny
make_phylogeny
 
 
make_prefs_file
make_prefs_file
 
 
make_qiime_py_file
make_qiime_py_file
 
 
make_rarefaction_plots
make_rarefaction_plots
 
 
make_tep
make_tep
 
 
map_reads_to_reference
map_reads_to_reference
 
 
merge_mapping_files
merge_mapping_files
 
 
merge_otu_maps
merge_otu_maps
 
 
merge_otu_tables
merge_otu_tables
 
 
multiple_rarefactions
multiple_rarefactions
 
 
multiple_rarefactions_even_depth
multiple_rarefactions_even_depth
 
 
neighbor_joining
neighbor_joining
 
 
nmds
nmds
 
 
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
pick_otus
 
 
pick_otus_through_otu_table
pick_otus_through_otu_table
 
 
pick_reference_otus_through_otu_table
pick_reference_otus_through_otu_table
 
 
pick_rep_set
pick_rep_set
 
 
pick_subsampled_reference_otus_through_otu_table
pick_subsampled_reference_otus_through_otu_table
 
 
plot_rank_abundance_graph
plot_rank_abundance_graph
 
 
plot_semivariogram
plot_semivariogram
 
 
plot_taxa_summary
plot_taxa_summary
 
 
poller
poller
 
 
principal_coordinates
principal_coordinates
 
 
quality_scores_plot
quality_scores_plot
 
 
relatedness
relatedness
 
 
shared_phylotypes
shared_phylotypes
 
 
simsam
simsam
 
 
single_rarefaction
single_rarefaction
 
 
sort_otu_table
sort_otu_table
 
 
split_fasta_on_sample_ids
split_fasta_on_sample_ids
 
 
split_libraries
split_libraries
 
 
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
 
 

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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 91.5%
  • Perl 4.2%
  • Shell 3.9%
  • Python 0.4%