Available Software

Here you will find our current processing recommendations.
Plugin Commands
ID 8: Visualization types, 0.1.0
Command Name Resource Allocation
ID 41: Generate HTML summary -p qiita -N 1 -n 1 --mem-per-cpu 8gb --time 50:00:00
ID 40: Validate -p qiita -N 1 -n 1 --mem 40gb --time 60:00:00
ID 11: QIIMEq2, 1.9.1
Command Name Resource Allocation
ID 58: Pick closed-reference OTUs -p qiita -N 1 -n 5 --mem 120gb --time 160:00:00
ID 59: Split libraries -p qiita -N 1 -n 1 --mem 60gb --time 25:00:00
ID 57: Trimming -p qiita -N 1 -n 1 --mem {input_size}+(4*(2**30)) --time 240:00:00
ID 60: Split libraries FASTQ -p qiita -N 1 -n 1 --mem 60gb --time 400:00:00
ID 15: BIOM type, 2.1.4 - Qiime2
Command Name Resource Allocation
ID 106: Validate -p qiita -N 1 -n 1 --mem 40gb --time 60:00:00
ID 107: Generate HTML summary -p qiita -N 1 -n 1 --mem-per-cpu 8gb --time 50:00:00
ID 40: qp-spades, 3.15.2
Command Name Resource Allocation
ID 539: spades -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 41: deblur, 2021.09
Command Name Resource Allocation
ID 540: Deblur 2021.09 -p qiita -N 1 -n 10 --mem ({input_size}*3)+(16*(2**30)) --time 400:00:00
ID 43: qtp-job-output-folder, 2021.08
Command Name Resource Allocation
ID 541: Validate -p qiita -N 1 -n 1 --mem 40gb --time 60:00:00
ID 542: Generate HTML summary -p qiita -N 1 -n 1 --mem-per-cpu 8gb --time 50:00:00
ID 45: qp-meta, 2021.11
Command Name Resource Allocation
ID 594: Sortmerna v2.1b -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 46: qp-fastp-minimap2, 2022.04
Command Name Resource Allocation
ID 596: Adapter and host filtering -p qiita -N 1 -n 1 --mem 16gb --time 240:00:00
ID 47: qp-klp, 2022.04
Command Name Resource Allocation
ID 595: Sequence Processing Pipeline -p qiita -N 1 -n 1 --mem 16gb --time 26:00:00
ID 50: Sequencing Data Type, 2022.11
Command Name Resource Allocation
ID 652: Validate -p qiita -N 1 -n 1 --mem 40gb --time 60:00:00
ID 653: Generate HTML summary -p qiita -N 1 -n 1 --mem-per-cpu 8gb --time 50:00:00
ID 51: qp-woltka, 2022.09
Command Name Resource Allocation
ID 654: Woltka v0.1.4 -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 52: Diversity types, 2023.02
Command Name Resource Allocation
ID 655: Validate -p qiita -N 1 -n 1 --mem 40gb --time 60:00:00
ID 656: Generate HTML summary -p qiita -N 1 -n 1 --mem-per-cpu 8gb --time 50:00:00
ID 54: qiime2, 2023.2.0
Command Name Resource Allocation
ID 726: Convert to relative frequencies [relative_frequency] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 745: Visualize taxonomy with an interactive bar plot [barplot] -p qiita -N 1 -n 1 --mem 24gb --time 100:00:00
ID 716: Alpha rarefaction curves [alpha_rarefaction] -p qiita -N 1 -n 1 --mem 60gb --time 400:00:00
ID 735: Filter features from a table based on abundance and prevalence [filter_features_conditionally] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 754: Beta diversity correlation [beta_correlation] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 732: Renames sample or feature ids in a table [rename_ids] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 751: Nonparametric microbial interdependence test [nmit] -p qiita -N 1 -n 1 --mem 48gb --time 250:00:00
ID 713: Pre-fitted sklearn-based taxonomy classifier [classify_sklearn] -p qiita -N 1 -n 5 --mem 200gb --time 150:00:00
ID 770: Filter features against reference [filter_features] -p qiita -N 1 -n 1 --mem 32gb --time 32:00:00
ID 742: Convert (and merge) positive numeric metadata (in)to feature table. [metatable] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 764: Run k-nearest-neighbors on a labeled distance matrix. [classify_samples_from_dist] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 714: Visualize and Interact with Principal Coordinates Analysis Biplot [biplot] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 757: adonis PERMANOVA test for beta group significance [adonis] -p qiita -N 1 -n 1 --mem 80gb --time 50:00:00
ID 755: Apply the Mantel test to two distance matrices [mantel] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 733: Summarize table [summarize] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 752: Apply ANCOM to identify features that differ in abundance. [ancom] -p qiita -N 1 -n 1 --mem 8gb --time 3-10:00:00
ID 771: Non V4 16S sequence assessment [non_v4_16s] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 738: Remove features from table if they're not present in tree. [filter_table] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 720: Core diversity metrics (non-phylogenetic) [core_metrics] -p qiita -N 1 -n 5 --mem 16gb --time 35:00:00
ID 721: Beta diversity (phylogenetic) [beta_phylogenetic] -p qiita -N 1 -n 5 --mem 50gb --time 35:00:00
ID 740: Split a feature table into training and testing sets. [split_table] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 739: Nested cross-validated supervised learning classifier. [classify_samples_ncv] -p qiita -N 1 -n 1 --mem 64gb --time 30:00:00
ID 759: t-distributed stochastic neighbor embedding [tsne] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 758: Filter samples from a distance matrix. [filter_distance_matrix] -p qiita -N 1 -n 1 --mem 16gb --time 50:00:00
ID 760: Uniform Manifold Approximation and Projection [umap] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 762: Paired pairwise distance testing and boxplots [pairwise_distances] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 744: Collapse features by their taxonomy at the specified level [collapse] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 746: Principal Coordinate Analysis Biplot [pcoa_biplot] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 763: Compute first distances or distance from baseline between sequential states [first_distances] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 715: Add pseudocount to table. [add_pseudocount] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 734: Subsample table [subsample] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 753: Principal Coordinate Analysis [pcoa] -p qiita -N 1 -n 1 --mem 70gb --time 50:00:00
ID 765: UMAP Embedding [embed] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 727: Generate a heatmap representation of a feature table [heatmap] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 766: Visualize and Interact with Principal Coordinates Analysis Plots [plot] -p qiita -N 1 -n 1 --mem 35gb --time 1:00:00
ID 767: Alpha diversity comparisons [alpha_group_significance] -p qiita -N 1 -n 1 --mem 25gb --time 100:00:00
ID 717: Beta diversity rarefaction [beta_rarefaction] -p qiita -N 1 -n 1 --mem 100gb --time 50:00:00
ID 750: Paired difference testing and boxplots [pairwise_differences] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 768: Alpha diversity correlation [alpha_correlation] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 769: Make a confusion matrix from sample classifier predictions. [confusion_matrix] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 736: Mislabelings against dataset [against_dataset] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 756: bioenv [bioenv] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 718: Beta diversity [beta] -p qiita -N 1 -n 1 --mem 40gb --time 400:00:00
ID 737: Mislabelings within dataset [within_dataset] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 719: Core diversity metrics (phylogenetic and non-phylogenetic) [core_metrics_phylogenetic] -p qiita -N 1 -n 5 --mem 40gb --time 35:00:00
ID 722: Alpha diversity [alpha] -p qiita -N 1 -n 1 --mem 32gb --time 30:00:00
ID 741: Nested cross-validated supervised learning regressor. [regress_samples_ncv] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 723: Alpha diversity (phylogenetic) [alpha_phylogenetic] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 761: Beta diversity group significance [beta_group_significance] -p qiita -N 1 -n 1 --mem 32gb --time 50:00:00
ID 724: Filter samples from table [filter_samples] -p qiita -N 1 -n 1 --mem 25gb --time 50:00:00
ID 743: Taxonomy-based feature table filter. [filter_table] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 725: Convert to presence/absence [presence_absence] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 728: Identify core features in table [core_features] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 747: Linear mixed effects modeling [linear_mixed_effects] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 729: Rarefy table [rarefy] -p qiita -N 1 -n 1 --mem 15gb --time 50:00:00
ID 748: Compute first differences or difference from baseline between sequential states [first_differences] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 730: Transpose a feature table. [transpose] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 749: Generate interactive volatility plot [volatility] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00
ID 731: Filter features from table [filter_features] -p qiita -N 1 -n 1 --mem 8gb --time 32:00:00