Pirate

Introduction

Pirate is a pangenome analysis and threshold evaluation toolbox.

For more information, please check its website: https://biocontainers.pro/tools/pirate and its home page on Github.

Versions

  • 1.0.4

Commands

  • PIRATE

  • FET.pl

  • PIRATE_to_Rtab.pl

  • PIRATE_to_roary.pl

  • SOAPsh.pl

  • ace.pl

  • analyse_blast_outputs.pl

  • analyse_loci_list.pl

  • annotate_treeWAS_output.pl

  • bamToGBrowse.pl

  • bdf2gdfont.pl

  • binhex.pl

  • bp_aacomp.pl

  • bp_biofetch_genbank_proxy.pl

  • bp_bioflat_index.pl

  • bp_biogetseq.pl

  • bp_blast2tree.pl

  • bp_bulk_load_gff.pl

  • bp_chaos_plot.pl

  • bp_classify_hits_kingdom.pl

  • bp_composite_LD.pl

  • bp_das_server.pl

  • bp_dbsplit.pl

  • bp_download_query_genbank.pl

  • bp_extract_feature_seq.pl

  • bp_fast_load_gff.pl

  • bp_fastam9_to_table.pl

  • bp_fetch.pl

  • bp_filter_search.pl

  • bp_find-blast-matches.pl

  • bp_flanks.pl

  • bp_gccalc.pl

  • bp_genbank2gff.pl

  • bp_genbank2gff3.pl

  • bp_generate_histogram.pl

  • bp_heterogeneity_test.pl

  • bp_hivq.pl

  • bp_hmmer_to_table.pl

  • bp_index.pl

  • bp_load_gff.pl

  • bp_local_taxonomydb_query.pl

  • bp_make_mrna_protein.pl

  • bp_mask_by_search.pl

  • bp_meta_gff.pl

  • bp_mrtrans.pl

  • bp_mutate.pl

  • bp_netinstall.pl

  • bp_nexus2nh.pl

  • bp_nrdb.pl

  • bp_oligo_count.pl

  • bp_parse_hmmsearch.pl

  • bp_process_gadfly.pl

  • bp_process_sgd.pl

  • bp_process_wormbase.pl

  • bp_query_entrez_taxa.pl

  • bp_remote_blast.pl

  • bp_revtrans-motif.pl

  • bp_search2alnblocks.pl

  • bp_search2gff.pl

  • bp_search2table.pl

  • bp_search2tribe.pl

  • bp_seq_length.pl

  • bp_seqconvert.pl

  • bp_seqcut.pl

  • bp_seqfeature_delete.pl

  • bp_seqfeature_gff3.pl

  • bp_seqfeature_load.pl

  • bp_seqpart.pl

  • bp_seqret.pl

  • bp_seqretsplit.pl

  • bp_split_seq.pl

  • bp_sreformat.pl

  • bp_taxid4species.pl

  • bp_taxonomy2tree.pl

  • bp_translate_seq.pl

  • bp_tree2pag.pl

  • bp_unflatten_seq.pl

  • cd-hit-2d-para.pl

  • cd-hit-clstr_2_blm8.pl

  • cd-hit-div.pl

  • cd-hit-para.pl

  • chrom_sizes.pl

  • clstr2tree.pl

  • clstr2txt.pl

  • clstr2xml.pl

  • clstr_cut.pl

  • clstr_list.pl

  • clstr_list_sort.pl

  • clstr_merge.pl

  • clstr_merge_noorder.pl

  • clstr_quality_eval.pl

  • clstr_quality_eval_by_link.pl

  • clstr_reduce.pl

  • clstr_renumber.pl

  • clstr_rep.pl

  • clstr_reps_faa_rev.pl

  • clstr_rev.pl

  • clstr_select.pl

  • clstr_select_rep.pl

  • clstr_size_histogram.pl

  • clstr_size_stat.pl

  • clstr_sort_by.pl

  • clstr_sort_prot_by.pl

  • clstr_sql_tbl.pl

  • clstr_sql_tbl_sort.pl

  • convert_to_distmat.pl

  • convert_to_treeWAS.pl

  • debinhex.pl

  • genomeCoverageBed.pl

  • legacy_blast.pl

  • make_multi_seq.pl

  • pangenome_variants_to_treeWAS.pl

  • paralogs_to_Rtab.pl

  • plot_2d.pl

  • plot_len1.pl

  • stag-autoschema.pl

  • stag-db.pl

  • stag-diff.pl

  • stag-drawtree.pl

  • stag-filter.pl

  • stag-findsubtree.pl

  • stag-flatten.pl

  • stag-grep.pl

  • stag-handle.pl

  • stag-itext2simple.pl

  • stag-itext2sxpr.pl

  • stag-itext2xml.pl

  • stag-join.pl

  • stag-merge.pl

  • stag-mogrify.pl

  • stag-parse.pl

  • stag-query.pl

  • stag-splitter.pl

  • stag-view.pl

  • stag-xml2itext.pl

  • stubmaker.pl

  • subsample_outputs.pl

  • subset_alignments.pl

  • unique_sequences.pl

  • update_blastdb.pl

Module

You can load the modules by:

module load biocontainers
module load pirate

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Pirate on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pirate
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers pirate