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qiime 1.4.0-2
  • links: PTS, VCS
  • area: main
  • in suites: wheezy
  • size: 29,704 kB
  • sloc: python: 77,837; haskell: 379; sh: 113; makefile: 103

Folder: scripts

d .. (parent)
- - rwxr-xr-x 2,172 add_taxa.py
- - rwxr-xr-x 2,313 adjust_seq_orientation.py
- - rwxr-xr-x 11,305 align_seqs.py
- - rwxr-xr-x 5,730 alpha_diversity.py
- - rwxr-xr-x 6,017 alpha_rarefaction.py
- - rwxr-xr-x 6,389 ampliconnoise.py
- - rwxr-xr-x 11,693 assign_taxonomy.py
- - rwxr-xr-x 7,315 beta_diversity.py
- - rwxr-xr-x 1,045 beta_diversity_through_3d_plots.py
- - rwxr-xr-x 7,152 beta_diversity_through_plots.py
- - rwxr-xr-x 6,109 beta_significance.py
- - rwxr-xr-x 2,476 blast_wrapper.py
- - rwxr-xr-x 5,832 categorized_dist_scatterplot.py
- - rwxr-xr-x 6,806 check_id_map.py
- - rwxr-xr-x 3,331 cluster_quality.py
- - rwxr-xr-x 5,873 collate_alpha.py
- - rwxr-xr-x 9,467 compare_3d_plots.py
- - rwxr-xr-x 3,479 compare_alpha_diversity.py
- - rwxr-xr-x 3,391 compare_distance_matrices.py
- - rwxr-xr-x 3,616 consensus_tree.py
- - rwxr-xr-x 1,966 convert_otu_table_to_unifrac_sample_mapping.py
- - rwxr-xr-x 1,834 convert_unifrac_sample_mapping_to_otu_table.py
- - rwxr-xr-x 8,564 core_qiime_analyses.py
- - rwxr-xr-x 3,178 count_seqs.py
- - rwxr-xr-x 6,140 denoise_wrapper.py
- - rwxr-xr-x 11,500 denoiser.py
- - rwxr-xr-x 5,330 denoiser_preprocess.py
- - rwxr-xr-x 3,032 denoiser_worker.py
- - rwxr-xr-x 2,785 dissimilarity_mtx_stats.py
- - rwxr-xr-x 3,053 distance_matrix_from_mapping.py
- - rwxr-xr-x 405 ec2Clean
- - rwxr-xr-x 257 ec2Dispatch
- - rwxr-xr-x 12,076 exclude_seqs_by_blast.py
- - rwxr-xr-x 4,593 extract_seqs_by_sample_id.py
- - rwxr-xr-x 6,854 filter_alignment.py
- - rwxr-xr-x 5,141 filter_by_metadata.py
- - rwxr-xr-x 4,018 filter_distance_matrix.py
- - rwxr-xr-x 5,650 filter_fasta.py
- - rwxr-xr-x 6,559 filter_otu_table.py
- - rwxr-xr-x 3,523 filter_otus_by_sample.py
- - rwxr-xr-x 3,933 filter_tree.py
- - rwxr-xr-x 1,518 fix_arb_fasta.py
- - rwxr-xr-x 10,125 identify_chimeric_seqs.py
- - rwxr-xr-x 1,740 identify_missing_files.py
- - rwxr-xr-x 3,373 inflate_denoiser_output.py
- - rwxr-xr-x 6,862 jackknifed_beta_diversity.py
- - rwxr-xr-x 9,842 make_2d_plots.py
- - rwxr-xr-x 23,038 make_3d_plots.py
- - rwxr-xr-x 2,106 make_bootstrapped_tree.py
- - rwxr-xr-x 15,659 make_distance_boxplots.py
- - rwxr-xr-x 16,289 make_distance_comparison_plots.py
- - rwxr-xr-x 12,224 make_distance_histograms.py
- - rwxr-xr-x 2,844 make_fastq.py
- - rwxr-xr-x 3,769 make_library_id_lists.py
- - rwxr-xr-x 8,972 make_otu_heatmap.py
- - rwxr-xr-x 9,341 make_otu_heatmap_html.py
- - rwxr-xr-x 7,907 make_otu_network.py
- - rwxr-xr-x 3,584 make_otu_table.py
- - rwxr-xr-x 2,524 make_per_library_sff.py
- - rwxr-xr-x 5,062 make_phylogeny.py
- - rwxr-xr-x 6,288 make_prefs_file.py
- - rwxr-xr-x 5,562 make_qiime_py_file.py
- - rwxr-xr-x 9,427 make_qiime_rst_file.py
- - rwxr-xr-x 9,331 make_rarefaction_plots.py
- - rwxr-xr-x 7,567 make_tep.py
- - rwxr-xr-x 2,213 merge_mapping_files.py
- - rwxr-xr-x 3,615 merge_otu_maps.py
- - rwxr-xr-x 2,522 merge_otu_tables.py
- - rwxr-xr-x 5,571 multiple_rarefactions.py
- - rwxr-xr-x 3,382 multiple_rarefactions_even_depth.py
- - rwxr-xr-x 2,557 neighbor_joining.py
- - rwxr-xr-x 3,185 nmds.py
- - rwxr-xr-x 19,247 otu_category_significance.py
- - rwxr-xr-x 10,510 parallel_align_seqs_pynast.py
- - rwxr-xr-x 8,372 parallel_alpha_diversity.py
- - rwxr-xr-x 10,879 parallel_assign_taxonomy_blast.py
- - rwxr-xr-x 10,360 parallel_assign_taxonomy_rdp.py
- - rwxr-xr-x 11,078 parallel_beta_diversity.py
- - rwxr-xr-x 9,856 parallel_blast.py
- - rwxr-xr-x 17,517 parallel_identify_chimeric_seqs.py
- - rwxr-xr-x 9,882 parallel_multiple_rarefactions.py
- - rwxr-xr-x 10,474 parallel_pick_otus_blast.py
- - rwxr-xr-x 12,111 parallel_pick_otus_uclust_ref.py
- - rwxr-xr-x 4,666 per_library_stats.py
- - rwxr-xr-x 32,421 pick_otus.py
- - rwxr-xr-x 5,899 pick_otus_through_otu_table.py
- - rwxr-xr-x 5,299 pick_reference_otus_through_otu_table.py
- - rwxr-xr-x 6,265 pick_rep_set.py
- - rwxr-xr-x 4,043 plot_rank_abundance_graph.py
- - rwxr-xr-x 8,088 plot_semivariogram.py
- - rwxr-xr-x 13,886 plot_taxa_summary.py
- - rwxr-xr-x 2,719 poller.py
- - rwxr-xr-x 5,694 poller_example.py
- - rwxr-xr-x 4,693 pool_by_metadata.py
- - rwxr-xr-x 3,202 principal_coordinates.py
- - rwxr-xr-x 27,991 print_qiime_config.py
- - rwxr-xr-x 5,288 process_iseq.py
- - rwxr-xr-x 3,352 process_qseq.py
- - rwxr-xr-x 2,949 process_sff.py
- - rwxr-xr-x 3,273 quality_scores_plot.py
- - rwxr-xr-x 4,147 shared_phylotypes.py
- - rwxr-xr-x 2,154 simsam.py
- - rwxr-xr-x 3,878 single_rarefaction.py
- - rwxr-xr-x 3,813 sort_otu_table.py
- - rwxr-xr-x 2,036 split_fasta_on_sample_ids.py
- - rwxr-xr-x 21,863 split_libraries.py
- - rwxr-xr-x 9,821 split_libraries_fastq.py
- - rwxr-xr-x 8,541 split_libraries_illumina.py
- - rwxr-xr-x 4,065 split_otu_table.py
- - rwxr-xr-x 2,455 split_otu_table_by_taxonomy.py
- - rwxr-xr-x 4,576 start_parallel_jobs.py
- - rwxr-xr-x 3,317 start_parallel_jobs_torque.py
- - rwxr-xr-x 2,872 submit_to_mgrast.py
- - rwxr-xr-x 1,964 subsample_fasta.py
- - rwxr-xr-x 3,082 summarize_otu_by_cat.py
- - rwxr-xr-x 10,130 summarize_taxa.py
- - rwxr-xr-x 4,966 summarize_taxa_through_plots.py
- - rwxr-xr-x 6,478 supervised_learning.py
- - rwxr-xr-x 5,798 transform_coordinate_matrices.py
- - rwxr-xr-x 3,287 tree_compare.py
- - rwxr-xr-x 2,182 trflp_file_to_otu_table.py
- - rwxr-xr-x 2,647 trim_sff_primers.py
- - rwxr-xr-x 2,830 truncate_fasta_qual_files.py
- - rwxr-xr-x 2,091 unweight_fasta.py
- - rwxr-xr-x 2,736 upgma_cluster.py