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 40: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 41: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 11: QIIMEq2, 1.9.1
Command Name Resource Allocation
ID 57: Trimming -q qiita -l nodes=1:ppn=1 -l mem={input_size}+(4*(2**30)) -l walltime=240:00:00
ID 58: Pick closed-reference OTUs -q qiita -l nodes=1:ppn=5 -l mem=120gb -l walltime=160:00:00
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 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 20: deblur, 1.1.0
Command Name Resource Allocation
ID 134: Deblur -q qiita -l nodes=1:ppn=5 -l mem=({input_size}*3)+(16*(2**30)) -l walltime=400:00:00
ID 24: Diversity types, 0.1.1
Command Name Resource Allocation
ID 185: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 186: 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 34: qiime2, 2020.11.1
Command Name Resource Allocation
ID 436: Taxonomy-based feature table filter. [filter_table] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 449: 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 455: Transpose a feature table. [transpose] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 482: Alpha diversity correlation [alpha_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 437: Visualize taxonomy with an interactive bar plot [barplot] -q qiita -l nodes=1:ppn=1 -l mem=24gb -l walltime=100:00:00
ID 450: 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 456: Rarefy table [rarefy] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 468: Paired difference testing and boxplots [pairwise_differences] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 469: Nonparametric microbial interdependence test [nmit] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 484: Pre-fitted sklearn-based taxonomy classifier [classify_sklearn] -q qiita -l nodes=1:ppn=5 -l mem=84gb -l walltime=150:00:00
ID 438: 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 451: Filter samples from table [filter_samples] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 457: Beta diversity (phylogenetic) [beta_phylogenetic] -q qiita -l nodes=1:ppn=5 -l mem=8gb -l walltime=35:00:00
ID 470: 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 439: 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 458: Alpha diversity (phylogenetic) [alpha_phylogenetic] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 440: Generate heatmap of important features. [heatmap] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 441: 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 452: 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 460: Core diversity metrics (non-phylogenetic) [core_metrics] -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=35:00:00
ID 475: 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 442: 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 453: Convert to relative frequencies [relative_frequency] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 461: 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 472: 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 476: Beta diversity group significance [beta_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 454: Filter features from table [filter_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 477: Principal Coordinate Analysis [pcoa] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 480: bioenv [bioenv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 443: 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 459: Beta diversity rarefaction [beta_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 462: Alpha diversity [alpha] -q qiita -l nodes=1:ppn=1 -l mem=16gb -l walltime=3:00:00
ID 444: 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 463: Beta diversity [beta] -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=35:00:00
ID 464: Alpha rarefaction curves [alpha_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=100:00:00
ID 483: Alpha diversity comparisons [alpha_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 445: Convert to presence/absence [presence_absence] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 465: Add pseudocount to table [add_pseudocount] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 446: Summarize table [summarize] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 447: Identify core features in table [core_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 448: Subsample table [subsample] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 466: Generate interactive volatility plot [volatility] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 467: Linear mixed effects modeling [linear_mixed_effects] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 471: 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 473: Paired pairwise distance testing and boxplots [pairwise_distances] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 474: 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 478: Beta diversity correlation [beta_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 481: 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 479: adonis PERMANOVA test for beta group significance [adonis] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 35: qp-fastp-minimap2, 2021.01
Command Name Resource Allocation
ID 485: Adapter and host filtering -q qiita -l nodes=1:ppn=15 -l mem=16gb -l walltime=240:00:00
ID 36: qp-meta, 2021.01
Command Name Resource Allocation
ID 486: Sortmerna v2.1b -q qiita -l nodes=1:ppn=10 -l mem=40gb -l walltime=500:00:00