Available Software

Here you will find our current processing recommendations.
Plugin Commands
ID 3: Target Gene type, 0.1.0
Command Name Resource Allocation
ID 7: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 6: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
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 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 59: Split libraries -q qiita -l nodes=1:ppn=1 -l mem=60gb -l walltime=25:00:00
ID 60: Split libraries FASTQ -q qiita -l nodes=1:ppn=1 -l mem=60gb -l walltime=400:00:00
ID 15: BIOM type, 2.1.4 - Qiime2
Command Name Resource Allocation
ID 107: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 106: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 20: deblur, 1.1.0
Command Name Resource Allocation
ID 134: Deblur -q qiita -l nodes=1:ppn=5 -l mem=({input_size}*3)+(13*(2**30)) -l walltime=400:00:00
ID 24: Diversity types, 0.1.1
Command Name Resource Allocation
ID 186: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 185: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 30: qp-shogun, 072020
Command Name Resource Allocation
ID 380: Atropos v1.1.24 -q qiita -l nodes=1:ppn=15 -l mem=30gb -l walltime=1000:00:00
ID 383: Sortmerna v2.1b -q qiita -l nodes=1:ppn=10 -l mem=40gb -l walltime=500:00:00
ID 382: Shogun v1.0.8 -q qiita -l nodes=1:ppn=24 -l mem=90gb -l walltime=400:00:00
ID 381: QC_Filter -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=310:00:00
ID 31: qiime2, 2020.8.0
Command Name Resource Allocation
ID 431: Pre-fitted sklearn-based taxonomy classifier [classify_sklearn] -q qiita -l nodes=1:ppn=5 -l mem=84gb -l walltime=150:00:00
ID 430: Alpha diversity correlation [alpha_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 429: Alpha diversity comparisons [alpha_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 428: 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 427: Filter samples from a distance matrix. [filter_distance_matrix] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 426: Principal Coordinate Analysis [pcoa] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 425: bioenv [bioenv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 424: Beta diversity group significance [beta_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 423: Beta diversity correlation [beta_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 422: adonis PERMANOVA test for beta group significance [adonis] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 421: 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 420: Paired pairwise distance testing and boxplots [pairwise_distances] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 419: 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 418: 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 417: Linear mixed effects modeling [linear_mixed_effects] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 416: Plot longitudinal feature volatility and importances [plot_feature_volatility] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 415: Nonparametric microbial interdependence test [nmit] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 414: Paired difference testing and boxplots [pairwise_differences] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 413: Generate interactive volatility plot [volatility] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 412: Add pseudocount to table [add_pseudocount] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 411: Beta diversity [beta] -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=35:00:00
ID 410: Alpha diversity [alpha] -q qiita -l nodes=1:ppn=1 -l mem=16gb -l walltime=3:00:00
ID 409: Beta diversity rarefaction [beta_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 408: Core diversity metrics (non-phylogenetic) [core_metrics] -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=35:00:00
ID 407: Beta diversity (phylogenetic) [beta_phylogenetic] -q qiita -l nodes=1:ppn=5 -l mem=8gb -l walltime=35:00:00
ID 406: Alpha diversity (phylogenetic) [alpha_phylogenetic] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 405: Alpha rarefaction curves [alpha_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=100:00:00
ID 404: 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 403: Filter samples from table [filter_samples] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 402: Subsample table [subsample] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 401: Summarize table [summarize] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 400: Rarefy table [rarefy] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 399: Identify core features in table [core_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 398: 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 397: Transpose a feature table. [transpose] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 396: Convert to relative frequencies [relative_frequency] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 395: Convert to presence/absence [presence_absence] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 394: Filter features from table [filter_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 393: 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 392: 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 391: Generate heatmap of important features. [heatmap] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 390: 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 389: 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 388: 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 387: Nested cross-validated supervised learning regressor. [regress_samples_ncv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 386: Taxonomy-based feature table filter. [filter_table] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 385: Visualize taxonomy with an interactive bar plot [barplot] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 384: 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