BV-BRC Command Line Program Reference

• Common Options to Command Line Programs
• GenomeTypeObject
• Hsp
• P3DataAPI
• P3Utils
• Sim
• appserv-enumerate-apps
• appserv-enumerate-tasks
• appserv-kill-task
• appserv-query-task
• appserv-rerun-task
• appserv-start-app
• p3-aggregates-to-html
• p3-all-contigs
• p3-all-drugs
• p3-all-genomes
• p3-all-subsystem-roles
• p3-all-subsystems
• p3-all-taxonomies
• p3-blast
• p3-build-kmer-db
• p3-cat
• p3-closest-seqs
• p3-co-occur
• p3-collate
• p3-compare-cols
• p3-count
• p3-count-families
• p3-cp
• p3-discriminating-kmers
• p3-dump-genomes
• p3-echo
• p3-extract
• p3-fasta-md5
• p3-feature-gap
• p3-feature-upstream
• p3-file-filter
• p3-find-couples
• p3-find-features
• p3-find-in-clusters
• p3-find-serology-data
• p3-find-surveillance-data
• p3-format-results
• p3-function-parse
• p3-function-to-role
• p3-generate-close-roles
• p3-generate-clusters
• p3-genome-distance
• p3-genome-fasta
• p3-genome-kmer-hits
• p3-genome-md5
• p3-genus-species
• p3-get-drug-genomes
• p3-get-family-data
• p3-get-family-features
• p3-get-feature-data
• p3-get-feature-group
• p3-get-feature-protein-regions
• p3-get-feature-protein-structures
• p3-get-feature-regions
• p3-get-feature-sequence
• p3-get-feature-subsystems
• p3-get-features-by-sequence
• p3-get-features-in-regions
• p3-get-genome-contigs
• p3-get-genome-data
• p3-get-genome-drugs
• p3-get-genome-expression
• p3-get-genome-features
• p3-get-genome-group
• p3-get-genome-protein-regions
• p3-get-genome-protein-structures
• p3-get-genome-refseq-features
• p3-get-genome-sp-genes
• p3-get-genome-subsystems
• p3-get-subsystem-features
• p3-get-subsystem-roles
• p3-get-taxonomy-data
• p3-gto
• p3-gto-dna
• p3-gto-fasta
• p3-gto-fetch
• p3-gto-scan
• p3-head
• p3-identify-clusters
• p3-job-status
• p3-join
• p3-kmer-compare
• p3-less
• p3-list-feature-groups
• p3-list-genome-groups
• p3-login
• p3-logout
• p3-ls
• p3-mass-cluster-run
• p3-match
• p3-merge
• p3-mkdir
• p3-nucleon-runs
• p3-peg-kmer-hits
• p3-pick
• p3-pick-by-class
• p3-pivot
• p3-project-subsystems
• p3-put-feature-group
• p3-put-genome-group
• p3-qstat
• p3-rast
• p3-related-by-clusters
• p3-rep-prots
• p3-rm
• p3-rmdir
• p3-role-fasta
• p3-role-features
• p3-role-matrix
• p3-sequence-profile
• p3-set-to-relation
• p3-shuffle
• p3-signature-clusters
• p3-signature-families
• p3-signature-peginfo
• p3-sort
• p3-stats
• p3-submit-BLAST
• p3-submit-CGA
• p3-submit-MSA
• p3-submit-codon-tree
• p3-submit-fastqutils
• p3-submit-gene-tree
• p3-submit-genome-annotation
• p3-submit-genome-assembly
• p3-submit-metagenome-binning
• p3-submit-metagenomic-read-mapping
• p3-submit-proteome-comparison
• p3-submit-rnaseq
• p3-submit-sars2-analysis
• p3-submit-sars2-assembly
• p3-submit-taxonomic-classification
• p3-submit-variation-analysis
• p3-subsys-roles
• p3-tail
• p3-tbl-to-fasta
• p3-tbl-to-html
• p3-tests
• p3-uni-roles
• p3-user-subsystem
• p3-whoami
• p3-write-kmers
• submit-patric-annotation
• submit-patric-genbank