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qiime 1.9.1+dfsg-3
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  • area: main
  • in suites: sid
  • size: 114,512 kB
  • sloc: python: 109,265; haskell: 379; makefile: 127; sh: 107

Folder: scripts

d .. (parent)
- - rwxr-xr-x 8,414 add_alpha_to_mapping_file.py
- - rwxr-xr-x 4,707 add_qiime_labels.py
- - rwxr-xr-x 2,370 adjust_seq_orientation.py
- - rwxr-xr-x 12,794 align_seqs.py
- - rwxr-xr-x 6,445 alpha_diversity.py
- - rwxr-xr-x 7,512 alpha_rarefaction.py
- - rwxr-xr-x 7,971 ampliconnoise.py
- - rwxr-xr-x 24,070 assign_taxonomy.py
- - rwxr-xr-x 7,585 beta_diversity.py
- - rwxr-xr-x 7,195 beta_diversity_through_plots.py
- - rwxr-xr-x 8,718 beta_significance.py
- - rwxr-xr-x 2,550 blast_wrapper.py
- - rwxr-xr-x 6,295 categorized_dist_scatterplot.py
- - rwxr-xr-x 434 check_id_map.py
- - rwxr-xr-x 3,352 clean_raxml_parsimony_tree.py
- - rwxr-xr-x 3,884 cluster_quality.py
- - rwxr-xr-x 4,974 collapse_samples.py
- - rwxr-xr-x 5,968 collate_alpha.py
- - rwxr-xr-x 12,083 compare_alpha_diversity.py
- - rwxr-xr-x 10,104 compare_categories.py
- - rwxr-xr-x 11,435 compare_distance_matrices.py
- - rwxr-xr-x 13,772 compare_taxa_summaries.py
- - rwxr-xr-x 9,042 compare_trajectories.py
- - rwxr-xr-x 6,667 compute_core_microbiome.py
- - rwxr-xr-x 7,463 compute_taxonomy_ratios.py
- - rwxr-xr-x 4,834 conditional_uncovered_probability.py
- - rwxr-xr-x 3,783 consensus_tree.py
- - rwxr-xr-x 4,857 convert_fastaqual_fastq.py
- - rwxr-xr-x 453 convert_unifrac_sample_mapping_to_otu_table.py
- - rwxr-xr-x 9,708 core_diversity_analyses.py
- - rwxr-xr-x 3,207 count_seqs.py
- - rwxr-xr-x 13,671 demultiplex_fasta.py
- - rwxr-xr-x 5,809 denoise_wrapper.py
- - rwxr-xr-x 11,085 denoiser.py
- - rwxr-xr-x 4,992 denoiser_preprocess.py
- - rwxr-xr-x 2,937 denoiser_worker.py
- - rwxr-xr-x 4,109 detrend.py
- - rwxr-xr-x 9,304 differential_abundance.py
- - rwxr-xr-x 2,969 dissimilarity_mtx_stats.py
- - rwxr-xr-x 5,334 distance_matrix_from_mapping.py
- - rwxr-xr-x 7,483 estimate_observation_richness.py
- - rwxr-xr-x 11,950 exclude_seqs_by_blast.py
- - rwxr-xr-x 10,539 extract_barcodes.py
- - rwxr-xr-x 2,515 extract_reads_from_interleaved_file.py
- - rwxr-xr-x 4,725 extract_seqs_by_sample_id.py
- - rwxr-xr-x 7,606 filter_alignment.py
- - rwxr-xr-x 4,587 filter_distance_matrix.py
- - rwxr-xr-x 7,965 filter_fasta.py
- - rwxr-xr-x 3,733 filter_otus_by_sample.py
- - rwxr-xr-x 6,417 filter_otus_from_otu_table.py
- - rwxr-xr-x 7,540 filter_samples_from_otu_table.py
- - rwxr-xr-x 3,566 filter_taxa_from_otu_table.py
- - rwxr-xr-x 4,358 filter_tree.py
- - rwxr-xr-x 2,193 fix_arb_fasta.py
- - rwxr-xr-x 19,081 group_significance.py
- - rwxr-xr-x 22,012 identify_chimeric_seqs.py
- - rwxr-xr-x 1,891 identify_missing_files.py
- - rwxr-xr-x 9,187 identify_paired_differences.py
- - rwxr-xr-x 3,643 inflate_denoiser_output.py
- - rwxr-xr-x 7,794 jackknifed_beta_diversity.py
- - rwxr-xr-x 9,044 join_paired_ends.py
- - rwxr-xr-x 3,322 load_remote_mapping_file.py
- - rwxr-xr-x 12,121 make_2d_plots.py
- - rwxr-xr-x 12,784 make_bipartite_network.py
- - rwxr-xr-x 2,265 make_bootstrapped_tree.py
- - rwxr-xr-x 13,895 make_distance_boxplots.py
- - rwxr-xr-x 19,361 make_distance_comparison_plots.py
- - rwxr-xr-x 2,933 make_fastq.py
- - rwxr-xr-x 3,984 make_library_id_lists.py
- - rwxr-xr-x 11,318 make_otu_heatmap.py
- - rwxr-xr-x 143 make_otu_heatmap_html.py
- - rwxr-xr-x 7,695 make_otu_network.py
- - rwxr-xr-x 5,034 make_otu_table.py
- - rwxr-xr-x 2,638 make_per_library_sff.py
- - rwxr-xr-x 5,094 make_phylogeny.py
- - rwxr-xr-x 6,399 make_prefs_file.py
- - rwxr-xr-x 7,732 make_qiime_py_file.py
- - rwxr-xr-x 11,857 make_rarefaction_plots.py
- - rwxr-xr-x 3,900 make_tep.py
- - rwxr-xr-x 9,492 map_reads_to_reference.py
- - rwxr-xr-x 2,614 merge_mapping_files.py
- - rwxr-xr-x 3,741 merge_otu_maps.py
- - rwxr-xr-x 2,242 merge_otu_tables.py
- - rwxr-xr-x 8,885 multiple_extract_barcodes.py
- - rwxr-xr-x 9,056 multiple_join_paired_ends.py
- - rwxr-xr-x 5,667 multiple_rarefactions.py
- - rwxr-xr-x 3,619 multiple_rarefactions_even_depth.py
- - rwxr-xr-x 9,817 multiple_split_libraries_fastq.py
- - rwxr-xr-x 2,590 neighbor_joining.py
- - rwxr-xr-x 3,669 nmds.py
- - rwxr-xr-x 8,084 normalize_table.py
- - rwxr-xr-x 11,195 observation_metadata_correlation.py
- - rwxr-xr-x 600 otu_category_significance.py
- - rwxr-xr-x 4,354 parallel_align_seqs_pynast.py
- - rwxr-xr-x 3,853 parallel_alpha_diversity.py
- - rwxr-xr-x 5,207 parallel_assign_taxonomy_blast.py
- - rwxr-xr-x 4,481 parallel_assign_taxonomy_rdp.py
- - rwxr-xr-x 4,489 parallel_assign_taxonomy_uclust.py
- - rwxr-xr-x 5,688 parallel_beta_diversity.py
- - rwxr-xr-x 4,961 parallel_blast.py
- - rwxr-xr-x 9,496 parallel_identify_chimeric_seqs.py
- - rwxr-xr-x 6,613 parallel_map_reads_to_reference.py
- - rwxr-xr-x 7,091 parallel_merge_otu_tables.py
- - rwxr-xr-x 4,935 parallel_multiple_rarefactions.py
- - rwxr-xr-x 4,456 parallel_pick_otus_blast.py
- - rwxr-xr-x 5,192 parallel_pick_otus_sortmerna.py
- - rwxr-xr-x 4,644 parallel_pick_otus_trie.py
- - rwxr-xr-x 6,014 parallel_pick_otus_uclust_ref.py
- - rwxr-xr-x 6,184 parallel_pick_otus_usearch61_ref.py
- - rwxr-xr-x 9,742 pick_closed_reference_otus.py
- - rwxr-xr-x 8,989 pick_de_novo_otus.py
- - rwxr-xr-x 24,851 pick_open_reference_otus.py
- - rwxr-xr-x 53,549 pick_otus.py
- - rwxr-xr-x 6,054 pick_rep_set.py
- - rwxr-xr-x 4,312 plot_rank_abundance_graph.py
- - rwxr-xr-x 14,998 plot_semivariogram.py
- - rwxr-xr-x 12,351 plot_taxa_summary.py
- - rwxr-xr-x 3,088 poller.py
- - rwxr-xr-x 4,902 principal_coordinates.py
- - rwxr-xr-x 2,819 print_metadata_stats.py
- - rwxr-xr-x 35,065 print_qiime_config.py
- - rwxr-xr-x 5,049 process_iseq.py
- - rwxr-xr-x 3,663 process_qseq.py
- - rwxr-xr-x 4,105 process_sff.py
- - rwxr-xr-x 3,526 quality_scores_plot.py
- - rwxr-xr-x 6,102 relatedness.py
- - rwxr-xr-x 4,080 shared_phylotypes.py
- - rwxr-xr-x 4,697 simsam.py
- - rwxr-xr-x 4,296 single_rarefaction.py
- - rwxr-xr-x 4,089 sort_otu_table.py
- - rwxr-xr-x 23,065 split_libraries.py
- - rwxr-xr-x 18,339 split_libraries_fastq.py
- - rwxr-xr-x 10,456 split_libraries_lea_seq.py
- - rwxr-xr-x 6,225 split_otu_table.py
- - rwxr-xr-x 4,238 split_otu_table_by_taxonomy.py
- - rwxr-xr-x 2,630 split_sequence_file_on_sample_ids.py
- - rwxr-xr-x 4,800 start_parallel_jobs.py
- - rwxr-xr-x 4,277 start_parallel_jobs_sc.py
- - rwxr-xr-x 5,511 start_parallel_jobs_slurm.py
- - rwxr-xr-x 4,084 start_parallel_jobs_torque.py
- - rwxr-xr-x 2,095 subsample_fasta.py
- - rwxr-xr-x 141 summarize_otu_by_cat.py
- - rwxr-xr-x 12,690 summarize_taxa.py
- - rwxr-xr-x 6,029 summarize_taxa_through_plots.py
- - rwxr-xr-x 11,477 supervised_learning.py
- - rwxr-xr-x 9,188 transform_coordinate_matrices.py
- - rwxr-xr-x 3,256 tree_compare.py
- - rwxr-xr-x 2,002 trflp_file_to_otu_table.py
- - rwxr-xr-x 2,751 trim_sff_primers.py
- - rwxr-xr-x 2,735 truncate_fasta_qual_files.py
- - rwxr-xr-x 4,506 truncate_reverse_primer.py
- - rwxr-xr-x 2,212 unweight_fasta.py
- - rwxr-xr-x 2,738 upgma_cluster.py
- - rwxr-xr-x 5,353 validate_demultiplexed_fasta.py
- - rwxr-xr-x 8,038 validate_mapping_file.py