QIIME scripts

• add_taxa.py – Add taxa to OTU table
• adjust_seq_orientation.py – Get the reverse complement of all sequences
• align_seqs.py – Align sequences using a variety of alignment methods
• alpha_diversity.py – Calculate alpha diversity on each sample in an otu table, using a variety of alpha diversity metrics
• alpha_diversity_metrics – List of available metrics
• alpha_rarefaction.py – A workflow script for performing alpha rarefaction
• ampliconnoise.py – Run AmpliconNoise
• assign_taxonomy.py – Assign taxonomy to each sequence
• beta_diversity.py – Calculate beta diversity (pairwise sample dissimilarity) on one or many otu tables
• beta_diversity_metrics – List of available metrics
• beta_diversity_through_3d_plots.py –
• beta_diversity_through_plots.py – A workflow script for computing beta diversity distance matrices and the corresponding 3D plots
• beta_significance.py – This script runs any of a set of common tests to determine if a sample is statistically significantly different from another sample
• blast_wrapper.py – Blast Interface
• categorized_dist_scatterplot.py – makes a figure representing average distances between samples, broken down by categories. I call it a ‘categorized distance scatterplot’
• check_id_map.py – Checks user’s metadata mapping file for required data, valid format
• cluster_quality.py – compute the quality of a cluster
• collate_alpha.py – Collate alpha diversity results
• compare_3d_plots.py – Plot several PCoA files on the same 3D plot
• compare_alpha_diversity.py – This script compares alpha diversities based on a t_two_sample test
• compare_distance_matrices.py – Script for computing Mantel correlations between as set of distance matrices
• consensus_tree.py – This script outputs a majority consensus tree given a collection of input trees.
• convert_otu_table_to_unifrac_sample_mapping.py – Convert a QIIME OTU table to a UniFrac sample mapping file
• convert_unifrac_sample_mapping_to_otu_table.py – Convert a UniFrac sample mapping file to an OTU table
• core_qiime_analyses.py – A workflow for running a core set of QIIME analyses.
• cytoscape_usage – Loading Results with Cytoscape
• denoise.py –
• denoise_wrapper.py – Denoise a flowgram file
• denoiser.py – Remove noise from 454 sequencing data
• denoiser_postprocess.py – Merge denoiser output with OTU picker output
• denoiser_preprocess.py – Run phase of denoiser algorithm: prefix clustering
• denoiser_worker.py – Start a denoiser worker process
• dissimilarity_mtx_stats.py – Calculate mean, median and standard deviation from a set of distance matrices
• exclude_seqs_by_blast.py – Exclude contaminated sequences using BLAST
• extract_seqs_by_sample_id.py – Extract sequences based on the SampleID
• filter_alignment.py – Filter sequence alignment by removing highly variable regions
• filter_by_metadata.py – Filter OTU table by removal of specified metadata
• filter_fasta.py – This script can be applied to remove sequences from a fasta file based on input criteria.
• filter_otu_table.py – Filters OTU table by minimum OTU count and number of samples or by taxonomy
• filter_otus_by_sample.py – Filter OTU mapping file and sequences by SampleIDs
• filter_tree.py – This script prunes a tree based on a set of tip names
• fix_arb_fasta.py – Reformat ARB FASTA files
• identify_chimeric_seqs.py – Identify chimeric sequences in input FASTA file
• identify_missing_files.py – This script checks for the existence expected file in parallel runs.
• inflate_denoiser_output.py – Inflate denoiser results so they can be passed directly to OTU pickers.
• jackknifed_beta_diversity.py – A workflow script for performing jackknifed UPGMA clustering and build jackknifed 2d and 3D PCoA plots.
• make_2d_plots.py – Make 2D PCoA Plots
• make_3d_plots.py – Make 3D PCoA plots
• make_bootstrapped_tree.py – Make bootstrapped tree
• make_distance_histograms.py – Make distance histograms
• make_fastq.py – Make fastq file for ERA submission from paired fasta and qual files
• make_library_id_lists.py – Make library id lists
• make_otu_heatmap.py – Make heatmap of OTU table
• make_otu_heatmap_html.py – Make heatmap of OTU table
• make_otu_network.py – Make an OTU network and calculate statistics
• make_otu_table.py – Make OTU table
• make_per_library_sff.py – Make per-library sff files from ID lists
• make_phylogeny.py – Make Phylogeny
• make_pie_charts.py –
• make_prefs_file.py – Generate preferences file
• make_qiime_py_file.py – Create python file
• make_qiime_rst_file.py – Make Sphinx RST file
• make_rarefaction_plots.py – Generate Rarefaction Plots
• make_tep.py – Makes TopiaryExplorer project file
• merge_denoiser_output.py – Merge the output of denoising step back into QIIME
• merge_mapping_files.py – Merge mapping files
• merge_otu_maps.py – Merge OTU mapping files
• merge_otu_tables.py – Merge two or more OTU tables into a single OTU table.
• multiple_rarefactions.py – Perform multiple subsamplings/rarefactions on an otu table
• multiple_rarefactions_even_depth.py – Perform multiple rarefactions on a single otu table, at one depth of sequences/sample
• neighbor_joining.py – Build a neighbor joining tree comparing samples
• nmds.py – Nonmetric Multidimensional Scaling (NMDS)
• otu_category_significance.py – OTU significance and co-occurence analysis
• parallel_align_seqs_pynast.py – Parallel sequence alignment using PyNAST
• parallel_alpha_diversity.py – Parallel alpha diversity
• parallel_assign_taxonomy_blast.py – Parallel taxonomy assignment using BLAST
• parallel_assign_taxonomy_rdp.py – Parallel taxonomy assignment using RDP
• parallel_beta_diversity.py – Parallel beta diversity
• parallel_blast.py – Parallel BLAST
• parallel_identify_chimeric_seqs.py – Parallel chimera detection
• parallel_multiple_rarefactions.py – Parallel multiple file rarefaction
• parallel_pick_otus_blast.py – Parallel pick otus using BLAST
• parallel_pick_otus_uclust_ref.py – Parallel pick otus using uclust_ref
• per_library_stats.py – Calculate per library statistics
• pick_otus.py – OTU picking
• pick_otus_through_otu_table.py – A workflow script for picking OTUs through building OTU tables
• pick_reference_otus_through_otu_table.py – Reference OTU picking/Shotgun UniFrac workflow.
• pick_rep_set.py – Pick representative set of sequences
• plot_rank_abundance_graph.py – plot rank-abundance curve
• plot_semivariogram.py – Fits a model between two distance matrices and plots the result
• plot_taxa_summary.py – Make taxaonomy summary charts based on taxonomy assignment
• poller.py – Poller for parallel QIIME scripts.
• poller_example.py – Create python file
• pool_by_metadata.py – pool samples in OTU table and mapping file based on sample metadata from mapping file
• preferences_file – Example of a prefs file
• principal_coordinates.py – Principal Coordinates Analysis (PCoA)
• print_qiime_config.py – Print out the qiime config settings.
• process_iseq.py – Given a directory of per-swath qseq files, this script generates a single fastq per lane.
• process_qseq.py – Given a directory of per-swath qseq files, this script generates a single fastq per lane.
• process_sff.py – Convert sff to FASTA and QUAL files
• quality_scores_plot.py – Generates histograms of sequence quality scores and number of nucleotides recorded at a particular index
• shared_phylotypes.py – Compute shared OTUs between all pairs of samples
• simsam.py – Simulate samples for each sample in an OTU table, using a phylogenetic tree.
• single_rarefaction.py – Perform rarefaction on an otu table
• sort_denoiser_output.py – Sort denoiser output by cluster size.
• sort_otu_table.py – Script for sorting the sample IDs in an OTU table based on a specified value in a mapping file.
• split_libraries.py – Split libraries according to barcodes specified in mapping file
• split_libraries_fastq.py – This script performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).
• split_libraries_illumina.py – Script for processing raw Illumina Genome Analyzer II data.
• split_otu_table.py – Split in a single OTU table into one OTU table per value in a specified field of the mapping file.
• split_otu_table_by_taxonomy.py – Script to split a single OTU table into multiple tables based on the taxonomy at some user-specified depth.
• start_parallel_jobs.py – Starts multiple jobs in parallel on multicore or multiprocessor systems.
• start_parallel_jobs_torque.py – Starts multiple jobs in parallel on torque/qsub based multiprocessor systems.
• submit_to_mgrast.py – This script submits a FASTA file to MG-RAST
• summarize_otu_by_cat.py – Summarize an OTU table by a single column in the mapping file.
• summarize_taxa.py – Summarize Taxa
• summarize_taxa_through_plots.py – A workflow script for performing taxonomy summaries and plots
• supervised_learning.py – Run supervised classification using OTUs as predictors and a mapping file category as class labels.
• transform_coordinate_matrices.py – Transform 2 coordinate matrices
• tree_compare.py – Compare jackknifed/bootstrapped trees
• trflp_file_to_otu_table.py – Convert TRFLP text file to an OTU table
• trim_sff_primers.py – Trim sff primers
• truncate_fasta_qual_files.py – Generates filtered fasta and quality score files by truncating at the specified base position.
• unweight_fasta.py – Transform fasta files with abundance weighting into unweighted
• upgma_cluster.py – Build a UPGMA tree comparing samples