QIIME 1 script to QIIME 2 action translation table
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QIIME 1 script nameQIIME 2 action name (or: NA, if not currently planned; Pending, if planned but not yet available; In progress, if currently in development; TBD, if currently undecided)Notes
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add_alpha_to_mapping_file.pySupported by being able to view SampleData[AlphaDiversity] as a MetadataCategory.
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add_qiime_labels.pyNAWill be supported by transformers.
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adjust_seq_orientation.pyNA
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align_seqs.pyqiime alignment mafft
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alpha_diversity.pyqiime diversity alpha; qiime diversity alpha-phylogenetic
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alpha_rarefaction.pyqiime diversity alpha-rarefaction
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ampliconnoise.pyNA
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assign_taxonomy.pyqiime feature-classifier classify-consensus-blast; qiime feature-classifier classify-consensus-vsearch; qiime feature-classifier classify-sklearn
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beta_diversity_through_plots.pyNAWill be included in "core diversity" Pipeline, functionality currently available through multiple steps.
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beta_diversity.pyqiime diversity beta; qiime diversity beta-phylogenetic
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beta_significance.pyNASee qiime diversity beta-correlation and qiime diversity beta-group-significance, which scale better to larger data sets.
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blast_wrapper.pyNA
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categorized_dist_scatterplot.pyNA
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clean_raxml_parsimony_tree.pyNA
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cluster_quality.pyNA
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collapse_samples.pyqiime feature-table group
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collate_alpha.pyqiime diversity alpha-rarefaction
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compare_alpha_diversity.pyqiime diversity alpha-group-significanceqiime diversity alpha-correlation is also likely of interest
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compare_categories.pyqiime diversity beta-group-significanceqiime diversity beta-correlation is also likely of interest
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compare_distance_matrices.pyPending
https://github.com/qiime2/q2-diversity/issues/94 ; qiime diversity beta-correlation is also likely of interest
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compare_taxa_summaries.pyNA
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compare_trajectories.pyTBDSeems useful if we can find a developer
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compute_core_microbiome.pyqiime feature-table core-features
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compute_taxonomy_ratios.pyTBDSeems useful if we can find a developer
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conditional_uncovered_probability.pyTBDSeems useful if we can find a developer
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consensus_tree.pyNA
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convert_fastaqual_fastq.pyNA
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convert_unifrac_sample_mapping_to_otu_table.pyNA
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core_diversity_analyses.pyBlocked (awaiting Pipelines)Many of the individual steps in this workflow are available in QIIME 2. Combining these steps into a single pipeline for convenience is pending.
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count_seqs.pyNAAvailable via summarize visualizers
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demultiplex_fasta.pyNA
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denoise_wrapper.pyNAbasic demultiplexing and quality control for 454 will be provided
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denoiser_preprocess.pyNAbasic demultiplexing and quality control for 454 will be provided
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denoiser_worker.pyNAbasic demultiplexing and quality control for 454 will be provided
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denoiser.pyNAbasic demultiplexing and quality control for 454 will be provided
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detrend.pyTBDSeems useful if we can find a developer
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differential_abundance.pyqiime gneiss ; qiime composition ancom
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dissimilarity_mtx_stats.pyNA
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distance_matrix_from_mapping.pyPending
https://github.com/qiime2/q2-metadata/issues/5 ; qiime diversity beta-correlation is also likely of interest
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estimate_observation_richness.pyNANeeds help from a statistician, if we think it would be useful (doesn't seem to be used by end users)
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exclude_seqs_by_blast.pyPendingqiime blast filter-features
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extract_barcodes.pyNAWill be supported by transformers.
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extract_reads_from_interleaved_file.pyNA
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extract_seqs_by_sample_id.pyNA
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filter_alignment.pyqiime alignment mask
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filter_distance_matrix.pyqiime diversity filter-distance-matrix
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filter_fasta.pyPending
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filter_otus_by_sample.pyPending
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filter_otus_from_otu_table.pyqiime feature-table filter-featuresqiime phylogeny filter-table is also likely of interest
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filter_samples_from_otu_table.pyqiime feature-table filter-samples
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filter_taxa_from_otu_table.pyqiime feature-table filter-featuresAdditional convenience method may be added in the future
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filter_tree.pyPendingqiime phylogeny filter-features
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fix_arb_fasta.pyNA
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group_significance.pyqiime gneiss ; qiime composition ancom
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identify_chimeric_seqs.pyPendingchimera filtering is incorporated in qiime dada2 denoise-*
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identify_missing_files.pyNA
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identify_paired_differences.pyqiime longitudinal pairwise-differences
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inflate_denoiser_output.pyNAbasic demultiplexing and quality control for 454 will be provided
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jackknifed_beta_diversity.pyIn progressqiime diversity beta-rarefaction
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join_paired_ends.pyPendingpaired-end joining is incorporated in qiime dada2 denoise-*
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load_remote_mapping_file.pyNAWill be supported where metadata can be provided
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make_2d_plots.pyIn progressWill be supported via qiime emperor plot
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make_bipartite_network.pyNAWill eventually be supported through a network analysis plugin
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make_bootstrapped_tree.pyNA
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make_distance_boxplots.pyqiime diversity beta-group-signifiance
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make_distance_comparison_plots.pyqiime diversity beta-group-signifiance
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make_fastq.pyNA
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make_library_id_lists.pyNA
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make_otu_heatmap_html.pyqiime gneiss dendrogram-heatmap
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make_otu_heatmap.pyqiime gneiss dendrogram-heatmap
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make_otu_network.pyNAWill eventually be supported through a network analysis plugin
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make_otu_table.pyqiime dada2 denoise-*; qiime deblur denoise
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make_per_library_sff.pyNAbasic demultiplexing and quality control for 454 will be provided
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make_phylogeny.pyqiime phylogeny fasttree
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make_prefs_file.pyNA
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make_qiime_py_file.pyhttps://docs.qiime2.org/2017.7/plugins/developing/This is replaced with plugin developer documentation
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make_rarefaction_plots.pyIn progressqiime diversity alpha-rarefaction
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make_tep.pyNA
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map_reads_to_reference.pyNAWill eventually be support by humann2 or other shotgun read mapping plugin
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merge_mapping_files.pyqiime metadata tabulate
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merge_otu_maps.pyNA
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merge_otu_tables.pyqiime feature-table mergeCan be improved when we support variadic inputs
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multiple_extract_barcodes.pyNA
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multiple_join_paired_ends.pyNApaired-end joining is incorporated in qiime dada2 denoise-*
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multiple_rarefactions_even_depth.pyIn progressqiime diversity alpha-rarefaction
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multiple_rarefactions.pyIn progressqiime diversity alpha-rarefaction
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multiple_split_libraries_fastq.pyNA
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neighbor_joining.pyPendingqiime diversity beta-rarefaction
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nmds.pyPendingqiime diversity nmds
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normalize_table.pyPendingNeeds developer familiar with DESeq2 and CSS
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observation_metadata_correlation.pyPendingqiime gneiss; qiime sample-classifier regress-samples (?)
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otu_category_significance.pyNAqiime gneiss, qiime composition ancom likely of interest
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parallel_align_seqs_pynast.pyNAPyNAST will not be supported, qiime alignment mafft likely of interest
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parallel_alpha_diversity.pyNAparallel functionality will be available in the same method as serial functionality
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parallel_assign_taxonomy_blast.pyNAparallel functionality will be available in the same method as serial functionality
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parallel_assign_taxonomy_rdp.pyNAparallel functionality will be available in the same method as serial functionality
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parallel_assign_taxonomy_uclust.pyNAparallel functionality will be available in the same method as serial functionality
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parallel_beta_diversity.pyNAparallel functionality will be available in the same method as serial functionality
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parallel_blast.pyNAparallel functionality will be available in the same method as serial functionality
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