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 -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 40: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 11: QIIMEq2, 1.9.1
Command Name Resource Allocation
ID 60: Split libraries FASTQ -q qiita -l nodes=1:ppn=1 -l mem=60gb -l walltime=400:00:00
ID 59: Split libraries -q qiita -l nodes=1:ppn=1 -l mem=60gb -l walltime=25:00:00
ID 58: Pick closed-reference OTUs -q qiita -l nodes=1:ppn=5 -l mem=120gb -l walltime=160:00:00
ID 57: Trimming -q qiita -l nodes=1:ppn=1 -l mem={input_size}+(4*(2**30)) -l walltime=240:00:00
ID 15: BIOM type, 2.1.4 - Qiime2
Command Name Resource Allocation
ID 106: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 107: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 33: qp-woltka, 2020.11
Command Name Resource Allocation
ID 435: Woltka v0.1.1 -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 37: Diversity types, 2021.05
Command Name Resource Allocation
ID 488: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 487: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 40: qp-spades, 3.15.2
Command Name Resource Allocation
ID 539: spades -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 41: deblur, 2021.09
Command Name Resource Allocation
ID 540: Deblur 2021.09 -q qiita -l nodes=1:ppn=10 -l mem=({input_size}*3)+(16*(2**30)) -l walltime=400:00:00
ID 43: qtp-job-output-folder, 2021.08
Command Name Resource Allocation
ID 541: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 542: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 45: qp-meta, 2021.11
Command Name Resource Allocation
ID 594: Sortmerna v2.1b -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 46: qp-fastp-minimap2, 2022.04
Command Name Resource Allocation
ID 596: Adapter and host filtering -q qiita -l nodes=1:ppn=1 -l mem=16gb -l walltime=240:00:00
ID 47: qp-klp, 2022.04
Command Name Resource Allocation
ID 595: Sequence Processing Pipeline -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 48: Sequencing Data Type, 2022.07
Command Name Resource Allocation
ID 650: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 651: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 49: qiime2, 2022.2.1
Command Name Resource Allocation
ID 597: Pre-fitted sklearn-based taxonomy classifier [classify_sklearn] -q qiita -l nodes=1:ppn=5 -l mem=200gb -l walltime=150:00:00
ID 607: Taxonomy-based feature table filter. [filter_table] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 632: Compute first differences or difference from baseline between sequential states [first_differences] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 599: Beta diversity rarefaction [beta_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=100gb -l walltime=50:00:00
ID 618: Summarize table [summarize] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 637: Beta diversity correlation [beta_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 600: Core diversity metrics (non-phylogenetic) [core_metrics] -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=35:00:00
ID 619: Filter samples from table [filter_samples] -q qiita -l nodes=1:ppn=1 -l mem=25gb -l walltime=50:00:00
ID 601: Core diversity metrics (phylogenetic and non-phylogenetic) [core_metrics_phylogenetic] -q qiita -l nodes=1:ppn=5 -l mem=40gb -l walltime=35:00:00
ID 620: Generate a heatmap representation of a feature table [heatmap] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 639: Apply the Mantel test to two distance matrices [mantel] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 602: Alpha diversity (phylogenetic) [alpha_phylogenetic] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 621: Convert to presence/absence [presence_absence] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 603: Beta diversity [beta] -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=400:00:00
ID 640: Filter samples from a distance matrix. [filter_distance_matrix] -q qiita -l nodes=1:ppn=1 -l mem=16gb -l walltime=50:00:00
ID 604: Alpha diversity [alpha] -q qiita -l nodes=1:ppn=1 -l mem=16gb -l walltime=30:00:00
ID 623: Convert (and merge) positive numeric metadata (in)to feature table. [metatable] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 605: Beta diversity (phylogenetic) [beta_phylogenetic] -q qiita -l nodes=1:ppn=5 -l mem=50gb -l walltime=35:00:00
ID 606: Collapse features by their taxonomy at the specified level [collapse] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 608: Visualize taxonomy with an interactive bar plot [barplot] -q qiita -l nodes=1:ppn=1 -l mem=24gb -l walltime=100:00:00
ID 624: Split a feature table into training and testing sets. [split_table] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 643: Compute first distances or distance from baseline between sequential states [first_distances] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 644: Run k-nearest-neighbors on a labeled distance matrix. [classify_samples_from_dist] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 609: Remove features from table if they're not present in tree. [filter_table] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 626: Nested cross-validated supervised learning classifier. [classify_samples_ncv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 627: Principal Coordinate Analysis Biplot [pcoa_biplot] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 628: Generate interactive volatility plot [volatility] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 647: Alpha diversity correlation [alpha_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 646: Visualize and Interact with Principal Coordinates Analysis Plots [plot] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 610: Add pseudocount to table [add_pseudocount] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 629: Linear mixed effects modeling [linear_mixed_effects] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 648: Alpha diversity comparisons [alpha_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=15gb -l walltime=100:00:00
ID 611: Renames sample or feature ids in a table [rename_ids] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 630: Paired difference testing and boxplots [pairwise_differences] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 649: Make a confusion matrix from sample classifier predictions. [confusion_matrix] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 613: Filter features from table [filter_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 612: Convert to relative frequencies [relative_frequency] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 631: Nonparametric microbial interdependence test [nmit] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 633: Uniform Manifold Approximation and Projection [umap] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 614: Subsample table [subsample] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 616: Filter features from a table based on abundance and prevalence [filter_features_conditionally] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 634: bioenv [bioenv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 645: UMAP Embedding [embed] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 635: t-distributed stochastic neighbor embedding [tsne] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 598: Alpha rarefaction curves [alpha_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=400:00:00
ID 617: Transpose a feature table. [transpose] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 636: Beta diversity group significance [beta_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 638: Principal Coordinate Analysis [pcoa] -q qiita -l nodes=1:ppn=1 -l mem=70gb -l walltime=50:00:00
ID 622: Rarefy table [rarefy] -q qiita -l nodes=1:ppn=1 -l mem=15gb -l walltime=50:00:00
ID 641: adonis PERMANOVA test for beta group significance [adonis] -q qiita -l nodes=1:ppn=1 -l mem=80gb -l walltime=50:00:00
ID 642: Paired pairwise distance testing and boxplots [pairwise_distances] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 615: Identify core features in table [core_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 625: Nested cross-validated supervised learning regressor. [regress_samples_ncv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00