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qiime 1.8.0%2Bdfsg-4
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd
  • size: 130,508 kB
  • ctags: 10,145
  • sloc: python: 110,826; haskell: 379; sh: 169; makefile: 125

Folder: scripts

d .. (parent)
- - rwxr-xr-x 7,423 add_alpha_to_mapping_file.py
- - rwxr-xr-x 4,632 add_qiime_labels.py
- - rwxr-xr-x 2,345 adjust_seq_orientation.py
- - rwxr-xr-x 12,538 align_seqs.py
- - rwxr-xr-x 6,094 alpha_diversity.py
- - rwxr-xr-x 7,056 alpha_rarefaction.py
- - rwxr-xr-x 7,320 ampliconnoise.py
- - rwxr-xr-x 21,110 assign_taxonomy.py
- - rwxr-xr-x 7,278 beta_diversity.py
- - rwxr-xr-x 6,944 beta_diversity_through_plots.py
- - rwxr-xr-x 7,628 beta_significance.py
- - rwxr-xr-x 2,479 blast_wrapper.py
- - rwxr-xr-x 5,975 categorized_dist_scatterplot.py
- - rwxr-xr-x 434 check_id_map.py
- - rwxr-xr-x 3,177 clean_raxml_parsimony_tree.py
- - rwxr-xr-x 3,620 cluster_quality.py
- - rwxr-xr-x 5,831 collate_alpha.py
- - rwxr-xr-x 9,540 compare_3d_plots.py
- - rwxr-xr-x 10,963 compare_alpha_diversity.py
- - rwxr-xr-x 9,361 compare_categories.py
- - rwxr-xr-x 10,341 compare_distance_matrices.py
- - rwxr-xr-x 12,370 compare_taxa_summaries.py
- - rwxr-xr-x 6,520 compute_core_microbiome.py
- - rwxr-xr-x 5,938 conditional_uncovered_probability.py
- - rwxr-xr-x 3,611 consensus_tree.py
- - rwxr-xr-x 4,887 convert_fastaqual_fastq.py
- - rwxr-xr-x 637 convert_otu_table_to_unifrac_sample_mapping.py
- - rwxr-xr-x 453 convert_unifrac_sample_mapping_to_otu_table.py
- - rwxr-xr-x 8,954 core_diversity_analyses.py
- - rwxr-xr-x 2,956 count_seqs.py
- - rwxr-xr-x 13,128 demultiplex_fasta.py
- - rwxr-xr-x 6,370 denoise_wrapper.py
- - rwxr-xr-x 11,168 denoiser.py
- - rwxr-xr-x 5,067 denoiser_preprocess.py
- - rwxr-xr-x 3,009 denoiser_worker.py
- - rwxr-xr-x 3,988 detrend.py
- - rwxr-xr-x 2,809 dissimilarity_mtx_stats.py
- - rwxr-xr-x 5,195 distance_matrix_from_mapping.py
- - rwxr-xr-x 405 ec2Clean
- - rwxr-xr-x 257 ec2Dispatch
- - rwxr-xr-x 7,273 estimate_observation_richness.py
- - rwxr-xr-x 12,161 exclude_seqs_by_blast.py
- - rwxr-xr-x 9,895 extract_barcodes.py
- - rwxr-xr-x 4,599 extract_seqs_by_sample_id.py
- - rwxr-xr-x 6,885 filter_alignment.py
- - rwxr-xr-x 4,243 filter_distance_matrix.py
- - rwxr-xr-x 8,404 filter_fasta.py
- - rwxr-xr-x 3,504 filter_otus_by_sample.py
- - rwxr-xr-x 6,132 filter_otus_from_otu_table.py
- - rwxr-xr-x 6,028 filter_samples_from_otu_table.py
- - rwxr-xr-x 3,260 filter_taxa_from_otu_table.py
- - rwxr-xr-x 3,874 filter_tree.py
- - rwxr-xr-x 2,104 fix_arb_fasta.py
- - rwxr-xr-x 18,794 group_significance.py
- - rwxr-xr-x 20,149 identify_chimeric_seqs.py
- - rwxr-xr-x 1,773 identify_missing_files.py
- - rwxr-xr-x 8,991 identify_paired_differences.py
- - rwxr-xr-x 3,477 inflate_denoiser_output.py
- - rwxr-xr-x 8,590 insert_seqs_into_tree.py
- - rwxr-xr-x 7,303 jackknifed_beta_diversity.py
- - rwxr-xr-x 9,074 join_paired_ends.py
- - rwxr-xr-x 3,213 load_remote_mapping_file.py
- - rwxr-xr-x 10,445 make_2d_plots.py
- - rwxr-xr-x 27,688 make_3d_plots.py
- - rwxr-xr-x 11,758 make_bipartite_network.py
- - rwxr-xr-x 2,107 make_bootstrapped_tree.py
- - rwxr-xr-x 12,436 make_distance_boxplots.py
- - rwxr-xr-x 18,807 make_distance_comparison_plots.py
- - rwxr-xr-x 12,735 make_distance_histograms.py
- - rwxr-xr-x 2,741 make_fastq.py
- - rwxr-xr-x 3,842 make_library_id_lists.py
- - rwxr-xr-x 9,734 make_otu_heatmap.py
- - rwxr-xr-x 9,217 make_otu_heatmap_html.py
- - rwxr-xr-x 7,564 make_otu_network.py
- - rwxr-xr-x 3,917 make_otu_table.py
- - rwxr-xr-x 2,555 make_per_library_sff.py
- - rwxr-xr-x 4,971 make_phylogeny.py
- - rwxr-xr-x 6,316 make_prefs_file.py
- - rwxr-xr-x 7,314 make_qiime_py_file.py
- - rwxr-xr-x 10,716 make_rarefaction_plots.py
- - rwxr-xr-x 3,773 make_tep.py
- - rwxr-xr-x 9,092 map_reads_to_reference.py
- - rwxr-xr-x 2,199 merge_mapping_files.py
- - rwxr-xr-x 3,668 merge_otu_maps.py
- - rwxr-xr-x 2,332 merge_otu_tables.py
- - rwxr-xr-x 5,499 multiple_rarefactions.py
- - rwxr-xr-x 3,467 multiple_rarefactions_even_depth.py
- - rwxr-xr-x 2,497 neighbor_joining.py
- - rwxr-xr-x 3,526 nmds.py
- - rwxr-xr-x 598 otu_category_significance.py
- - rwxr-xr-x 4,695 parallel_align_seqs_pynast.py
- - rwxr-xr-x 3,754 parallel_alpha_diversity.py
- - rwxr-xr-x 5,035 parallel_assign_taxonomy_blast.py
- - rwxr-xr-x 4,355 parallel_assign_taxonomy_rdp.py
- - rwxr-xr-x 4,290 parallel_assign_taxonomy_uclust.py
- - rwxr-xr-x 5,680 parallel_beta_diversity.py
- - rwxr-xr-x 4,750 parallel_blast.py
- - rwxr-xr-x 9,380 parallel_identify_chimeric_seqs.py
- - rwxr-xr-x 6,502 parallel_map_reads_to_reference.py
- - rwxr-xr-x 7,394 parallel_merge_otu_tables.py
- - rwxr-xr-x 4,953 parallel_multiple_rarefactions.py
- - rwxr-xr-x 4,450 parallel_pick_otus_blast.py
- - rwxr-xr-x 4,675 parallel_pick_otus_trie.py
- - rwxr-xr-x 5,996 parallel_pick_otus_uclust_ref.py
- - rwxr-xr-x 6,336 parallel_pick_otus_usearch61_ref.py
- - rwxr-xr-x 6,272 pick_closed_reference_otus.py
- - rwxr-xr-x 6,338 pick_de_novo_otus.py
- - rwxr-xr-x 12,666 pick_open_reference_otus.py
- - rwxr-xr-x 44,037 pick_otus.py
- - rwxr-xr-x 6,433 pick_rep_set.py
- - rwxr-xr-x 4,012 plot_rank_abundance_graph.py
- - rwxr-xr-x 12,824 plot_semivariogram.py
- - rwxr-xr-x 13,137 plot_taxa_summary.py
- - rwxr-xr-x 2,936 poller.py
- - rwxr-xr-x 5,671 poller_example.py
- - rwxr-xr-x 3,179 principal_coordinates.py
- - rwxr-xr-x 2,647 print_metadata_stats.py
- - rwxr-xr-x 36,247 print_qiime_config.py
- - rwxr-xr-x 5,262 process_iseq.py
- - rwxr-xr-x 3,397 process_qseq.py
- - rwxr-xr-x 3,918 process_sff.py
- - rwxr-xr-x 3,655 quality_scores_plot.py
- - rwxr-xr-x 5,487 relatedness.py
- - rwxr-xr-x 3,544 shared_phylotypes.py
- - rwxr-xr-x 4,514 simsam.py
- - rwxr-xr-x 4,036 single_rarefaction.py
- - rwxr-xr-x 4,193 sort_otu_table.py
- - rwxr-xr-x 2,126 split_fasta_on_sample_ids.py
- - rwxr-xr-x 21,978 split_libraries.py
- - rwxr-xr-x 16,967 split_libraries_fastq.py
- - rwxr-xr-x 3,566 split_otu_table.py
- - rwxr-xr-x 4,197 split_otu_table_by_taxonomy.py
- - rwxr-xr-x 4,726 start_parallel_jobs.py
- - rwxr-xr-x 4,167 start_parallel_jobs_sc.py
- - rwxr-xr-x 4,068 start_parallel_jobs_torque.py
- - rwxr-xr-x 2,889 submit_to_mgrast.py
- - rwxr-xr-x 1,997 subsample_fasta.py
- - rwxr-xr-x 4,994 summarize_otu_by_cat.py
- - rwxr-xr-x 12,150 summarize_taxa.py
- - rwxr-xr-x 5,844 summarize_taxa_through_plots.py
- - rwxr-xr-x 11,075 supervised_learning.py
- - rwxr-xr-x 7,930 transform_coordinate_matrices.py
- - rwxr-xr-x 3,058 tree_compare.py
- - rwxr-xr-x 2,021 trflp_file_to_otu_table.py
- - rwxr-xr-x 2,653 trim_sff_primers.py
- - rwxr-xr-x 2,672 truncate_fasta_qual_files.py
- - rwxr-xr-x 4,270 truncate_reverse_primer.py
- - rwxr-xr-x 2,082 unweight_fasta.py
- - rwxr-xr-x 2,650 upgma_cluster.py
- - rwxr-xr-x 5,169 validate_demultiplexed_fasta.py
- - rwxr-xr-x 7,772 validate_mapping_file.py