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 -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 60: Split libraries FASTQ -q qiita -l nodes=1:ppn=1 -l mem=60gb -l walltime=400:00:00
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 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 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 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
ID 37: Diversity types, 2021.05
Command Name Resource Allocation
ID 487: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 488: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 38: Sequencing Data Type, 2021.05
Command Name Resource Allocation
ID 537: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 538: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00
ID 39: qiime2, 2021.4.0
Command Name Resource Allocation
ID 498: Rarefy table [rarefy] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 497: 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 502: 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 504: Identify core features in table [core_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 489: Pre-fitted sklearn-based taxonomy classifier [classify_sklearn] -q qiita -l nodes=1:ppn=5 -l mem=84gb -l walltime=150:00:00
ID 516: Alpha diversity [alpha] -q qiita -l nodes=1:ppn=1 -l mem=16gb -l walltime=3:00:00
ID 518: Add pseudocount to table [add_pseudocount] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 492: 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 529: Principal Coordinate Analysis [pcoa] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 501: Convert to presence/absence [presence_absence] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 490: Visualize taxonomy with an interactive bar plot [barplot] -q qiita -l nodes=1:ppn=1 -l mem=24gb -l walltime=100:00:00
ID 505: Summarize table [summarize] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 500: 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 491: Taxonomy-based feature table filter. [filter_table] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 507: Subsample table [subsample] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 508: Filter samples from table [filter_samples] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 514: 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 509: Transpose a feature table. [transpose] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 506: Convert to relative frequencies [relative_frequency] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 513: Alpha diversity (phylogenetic) [alpha_phylogenetic] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 517: Beta diversity rarefaction [beta_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 521: Generate interactive volatility plot [volatility] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 520: Paired difference testing and boxplots [pairwise_differences] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 524: 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 526: 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 530: Beta diversity group significance [beta_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 532: adonis PERMANOVA test for beta group significance [adonis] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 495: 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 496: 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 499: 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 510: Beta diversity [beta] -q qiita -l nodes=1:ppn=5 -l mem=45gb -l walltime=35:00:00
ID 511: Core diversity metrics (non-phylogenetic) [core_metrics] -q qiita -l nodes=1:ppn=5 -l mem=16gb -l walltime=35:00:00
ID 531: bioenv [bioenv] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 527: Beta diversity correlation [beta_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 528: 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 533: 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 535: Alpha diversity correlation [alpha_correlation] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 534: Alpha diversity comparisons [alpha_group_significance] -q qiita -l nodes=1:ppn=1 -l mem=15gb -l walltime=100:00:00
ID 493: 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 503: Filter features from table [filter_features] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 515: Beta diversity (phylogenetic) [beta_phylogenetic] -q qiita -l nodes=1:ppn=5 -l mem=40gb -l walltime=35:00:00
ID 512: Alpha rarefaction curves [alpha_rarefaction] -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=400:00:00
ID 522: 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 519: Linear mixed effects modeling [linear_mixed_effects] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 523: Nonparametric microbial interdependence test [nmit] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 525: Paired pairwise distance testing and boxplots [pairwise_distances] -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 494: 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 40: qp-spades, 3.15.2
Command Name Resource Allocation
ID 539: spades -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 41: deblur, 2021.09
Command Name Resource Allocation
ID 540: Deblur 2021.09 -q qiita -l nodes=1:ppn=10 -l mem=({input_size}*3)+(16*(2**30)) -l walltime=400:00:00
ID 42: qp-klp, 2021.08
Command Name Resource Allocation
ID 543: Sequence Processing Pipeline -q qiita -l nodes=1:ppn=1 -l mem=8gb -l walltime=32:00:00
ID 43: qtp-job-output-folder, 2021.08
Command Name Resource Allocation
ID 541: Validate -q qiita -l nodes=1:ppn=1 -l mem=40gb -l walltime=60:00:00
ID 542: Generate HTML summary -q qiita -l nodes=1:ppn=1 -l pmem=8gb -l walltime=50:00:00