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 58: Pick closed-reference OTUs -p qiita -N 1 -n 1 --mem (5*(2**30))+({input_size}*3) --time 3600+({input_size}/60000)
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 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 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 541: Validate -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 542: Generate HTML summary -p qiita -N 1 -n 1 --mem 500mb --time 3:00:00
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 50: Sequencing Data Type, 2022.11
Command Name Resource Allocation
ID 653: Generate HTML summary -p qiita -N 1 -n 1 --mem 500mb --time 3:00:00
ID 652: Validate -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 5-00:00:00
ID 59: qiime2, 2023.5.1.2
Command Name Resource Allocation
ID 886: 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 875: 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 893: Make a confusion matrix from sample classifier predictions. [confusion_matrix] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 851: Filter features from table [filter_features] -p qiita -N 1 -n 1 --mem 500mb --time 00:10:00
ID 857: Summarize table [summarize] -p qiita -N 1 -n 1 --mem 4gb --time 00:10:00
ID 874: Generate interactive volatility plot [volatility] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 866: Nested cross-validated supervised learning classifier. [classify_samples_ncv] -p qiita -N 1 -n 1 --mem 64gb --time 30:00:00
ID 880: adonis PERMANOVA test for beta group significance [adonis] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 856: Filter samples from table [filter_samples] -p qiita -N 1 -n 1 --mem 4g --time 15
ID 877: Beta diversity group significance [beta_group_significance] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 887: Paired pairwise distance testing and boxplots [pairwise_distances] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 873: Linear mixed effects modeling [linear_mixed_effects] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 872: Nonparametric microbial interdependence test [nmit] -p qiita -N 1 -n 1 --mem 48gb --time 250:00:00
ID 888: 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 839: Add pseudocount to table. [add_pseudocount] -p qiita -N 1 -n 1 --mem 4gb --time 00:15:00
ID 858: Transpose a feature table. [transpose] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 852: Subsample table [subsample] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 892: Alpha diversity correlation [alpha_correlation] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 837: Pre-fitted sklearn-based taxonomy classifier [classify_sklearn] -p qiita -N 1 -n 1 --mem 45g --time 3-12:00:00
ID 848: Identify core features in table [core_features] -p qiita -N 1 -n 1 --mem 4gb --time 2:00:00
ID 869: Visualize taxonomy with an interactive bar plot [barplot] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 838: Visualize and Interact with Principal Coordinates Analysis Biplot [biplot] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 840: Alpha diversity (phylogenetic) [alpha_phylogenetic] -p qiita -N 1 -n 1 --mem 14g --time 6
ID 867: Taxonomy-based feature table filter. [filter_table] -p qiita -N 1 -n 1 --mem 4gb --time 00:20:00
ID 855: 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 845: Alpha rarefaction curves [alpha_rarefaction] -p qiita -N 1 -n 1 --mem (2**32)+(({samples}*{columns}*{input_size})/20000) --time 1500
ID 878: Uniform Manifold Approximation and Projection [umap] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 859: Convert to relative frequencies [relative_frequency] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 876: Apply ANCOM to identify features that differ in abundance. [ancom] -p qiita -N 1 -n 1 --mem 7gb --time 40:00:00
ID 879: t-distributed stochastic neighbor embedding [tsne] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 889: UMAP Embedding [embed] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 860: Mislabelings within dataset [within_dataset] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 868: Collapse features by their taxonomy at the specified level [collapse] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 847: Beta diversity rarefaction [beta_rarefaction] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 853: Renames sample or feature ids in a table [rename_ids] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 865: Convert (and merge) positive numeric metadata (in)to feature table. [metatable] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 843: Beta diversity [beta] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 870: Principal Coordinate Analysis Biplot [pcoa_biplot] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 844: Core diversity metrics (phylogenetic and non-phylogenetic) [core_metrics_phylogenetic] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 841: 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 854: Generate a heatmap representation of a feature table [heatmap] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 861: Mislabelings against dataset [against_dataset] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 871: Paired difference testing and boxplots [pairwise_differences] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 885: Principal Coordinate Analysis [pcoa] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 894: Filter features against reference [filter_features] -p qiita -N 1 -n 1 --mem 13gb --time 1:00:00
ID 895: Non V4 16S sequence assessment [non_v4_16s] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 849: 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 883: bioenv [bioenv] -p qiita -N 1 -n 1 --mem 6gb --time 1:00:00
ID 842: Core diversity metrics (non-phylogenetic) [core_metrics] -p qiita -N 1 -n 1 --mem 6gb --time 1:00:00
ID 862: 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 884: Filter samples from a distance matrix. [filter_distance_matrix] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 846: Alpha diversity [alpha] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 881: Apply the Mantel test to two distance matrices [mantel] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 863: Nested cross-validated supervised learning regressor. [regress_samples_ncv] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 891: Alpha diversity comparisons [alpha_group_significance] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 850: Convert to presence/absence [presence_absence] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 890: 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 882: Beta diversity correlation [beta_correlation] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 864: Split a feature table into training and testing sets. [split_table] -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 60: qp-fastp-minimap2, 2023.12.3
Command Name Resource Allocation
ID 896: Adapter and host filtering v2023.12 -p qiita -N 1 -n 1 --mem 16gb --time 240:00:00
ID 61: qp-qebil, 2023.04
Command Name Resource Allocation
ID 62: qp-woltka, 2023.11.1
Command Name Resource Allocation
ID 897: Woltka v0.1.4 -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 898: SynDNA Woltka -p qiita -N 1 -n 1 --mem 4gb --time 4:00:00
ID 899: Calculate Cell Counts -p qiita -N 1 -n 1 --mem 20gb --time 12:00:00
ID 900: Calculate RNA Copy Counts -p qiita -N 1 -n 1 --mem 20gb --time 12:00:00