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 3:00:00
ID 11: QIIMEq2, 1.9.1
Command Name Resource Allocation
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 58: Pick closed-reference OTUs -p qiita -N 1 -n 1 --mem (5*(2**30))+({input_size}*3) --time 3600+({input_size}/60000)
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 3:00:00
ID 40: qp-spades, 3.15.2
Command Name Resource Allocation
ID 539: spades -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
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 3:00:00
ID 541: Validate -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 45: qp-meta, 2021.11
Command Name Resource Allocation
ID 594: Sortmerna v2.1b -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
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 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 3:00:00
ID 51: qp-woltka, 2022.09
Command Name Resource Allocation
ID 654: Woltka v0.1.4 -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
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 3:00:00
ID 55: qp-klp, 2023.05
Command Name Resource Allocation
ID 772: Sequence Processing Pipeline -p qiita -N 1 -n 1 --mem {samples}*10000000--time 1020
ID 56: qiime2, 2023.5.1
Command Name Resource Allocation
ID 775: Add pseudocount to table. [add_pseudocount] -p qiita -N 1 -n 1 --mem 4gb --time 00:15:00
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 786: Summarize table [summarize] -p qiita -N 1 -n 1 --mem 4gb --time 00:10:00
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 779: Core diversity metrics (phylogenetic and non-phylogenetic) [core_metrics_phylogenetic] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 781: Alpha diversity [alpha] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 782: Alpha diversity (phylogenetic) [alpha_phylogenetic] -p qiita -N 1 -n 1 --mem 14g --time 6
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 4gb --time 4:00:00
ID 780: Beta diversity [beta] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
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**32)+(({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