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We will update the system on Tuesday July 15, 2025. No new jobs will start from the Friday before until the new version is deployed. Please plan accordingly.

Available Software

Here you will find our current processing recommendations.
Plugin Commands
ID 8: Visualization types, 0.1.0
Command Name Resource Allocation
ID 40: Validate -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 41: Generate HTML summary -p qiita -N 1 -n 1 --mem 500mb --time 12:00:00
ID 11: QIIMEq2, 1.9.1
Command Name Resource Allocation
ID 58: Pick closed-reference OTUs -p qiita -N 1 -n 1 --mem (5*(2**30))+({input_size}*3) --time 3600+({input_size}/60000)
ID 57: Trimming -p qiita -N 1 -n 1 --mem 2*(2**30)+{input_size} if 2*(2**30)+{input_size} < 16*(2**30) else 16*(2**30) --time 600
ID 59: Split libraries -p qiita -N 1 -n 1 --mem 60gb --time 25:00:00
ID 60: Split libraries FASTQ -p qiita -N 1 -n 1 --mem (3*(2**30))+({input_size}*0.4) if (3*(2**30))+({input_size}*0.4) < 50*(2**30) else 50*(2**30) --time 1000+({input_size}/700000)
ID 15: BIOM type, 2.1.4 - Qiime2
Command Name Resource Allocation
ID 106: Validate -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 107: Generate HTML summary -p qiita -N 1 -n 1 --mem 500mb --time 12:00:00
ID 41: deblur, 2021.09
Command Name Resource Allocation
ID 540: Deblur 2021.09 -p qiita -N 1 -n 10 --mem (14*(2**30))+(({samples}+{input_size})*5) if (14*(2**30))+(({samples}+{input_size})*5) < 70*(2**30) else 70*(2**30) --time (({samples}+{input_size})/nlog({samples}+{input_size})/360) if (({samples}+{input_size})/nlog({samples}+{input_size})/360) < 90000 else 90000
ID 43: qtp-job-output-folder, 2021.08
Command Name Resource Allocation
ID 542: Generate HTML summary -p qiita -N 1 -n 1 --mem 500mb --time 12:00:00
ID 541: Validate -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 50: Sequencing Data Type, 2022.11
Command Name Resource Allocation
ID 652: Validate -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 653: Generate HTML summary -p qiita -N 1 -n 1 --mem 500mb --time 12:00:00
ID 52: Diversity types, 2023.02
Command Name Resource Allocation
ID 655: Validate -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 656: Generate HTML summary -p qiita -N 1 -n 1 --mem 500mb --time 12:00:00
ID 56: qiime2, 2023.5.1
Command Name Resource Allocation
ID 779: Core diversity metrics (phylogenetic and non-phylogenetic) [core_metrics_phylogenetic] -p qiita -N 1 -n 1 --mem 100gb --time 12:00:00
ID 776: Core diversity metrics (non-phylogenetic) [core_metrics] -p qiita -N 1 -n 1 --mem 6gb --time 1:00:00
ID 774: Visualize and Interact with Principal Coordinates Analysis Biplot [biplot] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 775: Add pseudocount to table. [add_pseudocount] -p qiita -N 1 -n 1 --mem 4gb --time 00:15:00
ID 812: Apply ANCOM to identify features that differ in abundance. [ancom] -p qiita -N 1 -n 1 --mem 7gb --time 40:00:00
ID 783: Beta diversity (phylogenetic) [beta_phylogenetic] -p qiita -N 1 -n 5 --mem 13*(2**30)+({input_size}*8) if 13*(2**30)+({input_size}*8) < 21474836480 else 21474836480 --time 1000+{input_size}/80000 if 1000+{input_size}/80000 < 36000 else 36000
ID 782: Alpha diversity (phylogenetic) [alpha_phylogenetic] -p qiita -N 1 -n 1 --mem 16g --time 6
ID 781: Alpha diversity [alpha] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 786: Summarize table [summarize] -p qiita -N 1 -n 1 --mem 4gb --time 00:10:00
ID 773: Pre-fitted sklearn-based taxonomy classifier [classify_sklearn] -p qiita -N 1 -n 1 --mem 45g --time 3-12:00:00
ID 820: Principal Coordinate Analysis [pcoa] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 795: Filter features from a table based on abundance and prevalence [filter_features_conditionally] -p qiita -N 1 -n 1 --mem 1gb --time 00:10:00
ID 778: Beta diversity rarefaction [beta_rarefaction] -p qiita -N 1 -n 1 --mem 16gb --time 10:00:00
ID 780: Beta diversity [beta] -p qiita -N 1 -n 1 --mem 8gb --time 10:00:00
ID 802: Nested cross-validated supervised learning regressor. [regress_samples_ncv] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 817: bioenv [bioenv] -p qiita -N 1 -n 1 --mem 6gb --time 1:00:00
ID 777: Alpha rarefaction curves [alpha_rarefaction] -p qiita -N 1 -n 1 --mem (2**34)+(({samples}*{columns}*{input_size})/20000) --time 1500
ID 800: Convert (and merge) positive numeric metadata (in)to feature table. [metatable] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 814: Filter samples from a distance matrix. [filter_distance_matrix] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 790: Subsample table [subsample] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 805: Taxonomy-based feature table filter. [filter_table] -p qiita -N 1 -n 1 --mem 4gb --time 00:20:00
ID 822: Paired pairwise distance testing and boxplots [pairwise_distances] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 789: Renames sample or feature ids in a table [rename_ids] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 804: Collapse features by their taxonomy at the specified level [collapse] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 823: Compute first distances or distance from baseline between sequential states [first_distances] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 788: Identify core features in table [core_features] -p qiita -N 1 -n 1 --mem 4gb --time 2:00:00
ID 803: Visualize taxonomy with an interactive bar plot [barplot] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 824: Run k-nearest-neighbors on a labeled distance matrix. [classify_samples_from_dist] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 784: Convert to relative frequencies [relative_frequency] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 806: Principal Coordinate Analysis Biplot [pcoa_biplot] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 825: UMAP Embedding [embed] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 794: Filter features from table [filter_features] -p qiita -N 1 -n 1 --mem 500mb --time 00:10:00
ID 809: Compute first differences or difference from baseline between sequential states [first_differences] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 827: Alpha diversity comparisons [alpha_group_significance] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 792: Convert to presence/absence [presence_absence] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 807: Generate interactive volatility plot [volatility] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 828: Alpha diversity correlation [alpha_correlation] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 785: Filter samples from table [filter_samples] -p qiita -N 1 -n 1 --mem 4g --time 15
ID 810: Paired difference testing and boxplots [pairwise_differences] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 829: Make a confusion matrix from sample classifier predictions. [confusion_matrix] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 787: Generate a heatmap representation of a feature table [heatmap] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 808: Nonparametric microbial interdependence test [nmit] -p qiita -N 1 -n 1 --mem 48gb --time 250:00:00
ID 830: Filter features against reference [filter_features] -p qiita -N 1 -n 1 --mem 13gb --time 1:00:00
ID 791: Transpose a feature table. [transpose] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 813: Apply the Mantel test to two distance matrices [mantel] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 793: Rarefy table [rarefy] -p qiita -N 1 -n 1 --mem (2**31)+({input_size}*6) if (2**31)+({input_size}*6) < 13958643712 else 13958643712 --time 40
ID 818: Uniform Manifold Approximation and Projection [umap] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 797: Mislabelings within dataset [within_dataset] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 816: Beta diversity group significance [beta_group_significance] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 796: Mislabelings against dataset [against_dataset] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 821: adonis PERMANOVA test for beta group significance [adonis] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 798: Remove features from table if they're not present in tree. [filter_table] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 819: t-distributed stochastic neighbor embedding [tsne] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 801: Nested cross-validated supervised learning classifier. [classify_samples_ncv] -p qiita -N 1 -n 1 --mem 64gb --time 30:00:00
ID 815: Beta diversity correlation [beta_correlation] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 799: Split a feature table into training and testing sets. [split_table] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 811: Linear mixed effects modeling [linear_mixed_effects] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 826: Visualize and Interact with Principal Coordinates Analysis Plots [plot] -p qiita -N 1 -n 1 --mem (2**33)+(2**30)+(({samples}*{columns}*{input_size})/4500000) --time 30
ID 831: Non V4 16S sequence assessment [non_v4_16s] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 57: qp-fastp-minimap2, 2023.12
Command Name Resource Allocation
ID 832: Adapter and host filtering v2023.12 -p qiita -N 1 -n 1 --mem 16gb --time 240:00:00
ID 59: qp-meta, 2024.10
Command Name Resource Allocation
ID 837: SortMeRNA v4.3.7 -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 60: qp-woltka, 2024.09
Command Name Resource Allocation
ID 843: Remove SynDNA inserts & plasmid reads -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 845: Remove SynDNA plasmid, insert, & CP026085 reads -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 838: Woltka v0.1.7, paired-end -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 841: Calculate RNA Copy Counts -p qiita -N 1 -n 1 --mem 20gb --time 12:00:00
ID 839: Remove SynDNA reads -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 840: Calculate Cell Counts -p qiita -N 1 -n 1 --mem 20gb --time 12:00:00
ID 61: qp-klp, 2024.11
Command Name Resource Allocation
ID 842: Sequence Processing Pipeline -p qiita -N 1 -n 1 --mem 4g --time 5-00:00:00
ID 62: qp-spades, 2025.02
Command Name Resource Allocation
ID 844: cloudSPAdes -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00