Provided by: busco_5.4.3-1_all bug


       busco - benchmarking sets of universal single-copy orthologs


       usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]

       Welcome  to  BUSCO 5.2.2: the Benchmarking Universal Single-Copy Ortholog assessment tool.
       For more detailed usage information, please review the  README  file  provided  with  this
       distribution      and      the      BUSCO      user     guide.     Visit     this     page to see how to cite BUSCO

   optional arguments:
              Input sequence file in FASTA format. Can be an assembled  genome  or  transcriptome
              (DNA), or protein sequences from an annotated gene set. Also possible to use a path
              to a directory containing multiple input files.

       -o OUTPUT, --out OUTPUT
              Give your analysis run a recognisable short name. Output folders and files will  be
              labelled with this name. WARNING: do not provide a path

       -m MODE, --mode MODE
              Specify  which  BUSCO analysis mode to run.  There are three valid modes: - geno or
              genome, for genome assemblies (DNA) -  tran  or  transcriptome,  for  transcriptome
              assemblies (DNA) - prot or proteins, for annotated gene sets (protein)

       -l LINEAGE, --lineage_dataset LINEAGE
              Specify the name of the BUSCO lineage to be used.

              Use augustus gene predictor for eukaryote runs

       --augustus_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
              Pass  additional  arguments to Augustus. All arguments should be contained within a
              single pair of quotation marks, separated by commas.

       --augustus_species AUGUSTUS_SPECIES
              Specify a species for Augustus training.

              Run auto-lineage to find optimum lineage path

              Run auto-placement just on eukaryote tree to find optimum lineage path

              Run auto-lineage just on non-eukaryote trees to find optimum lineage path

       -c N, --cpu N
              Specify the number (N=integer) of threads/cores to use.

       --config CONFIG_FILE
              Provide a config file

       --datasets_version DATASETS_VERSION
              Specify the version of BUSCO datasets, e.g. odb10

       --download [dataset ...]
              Download dataset. Possible values are a specific dataset name, "all", "prokaryota",
              "eukaryota",  or  "virus". If used together with other command line arguments, make
              sure to place this last.

       --download_base_url DOWNLOAD_BASE_URL
              Set the url to the remote BUSCO dataset location

       --download_path DOWNLOAD_PATH
              Specify local filepath for storing BUSCO dataset downloads

       -e N, --evalue N
              E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03 (Default: 1e-03)

       -f, --force
              Force rewriting of existing files. Must be used when output files with the provided
              name already exist.

       -h, --help
              Show this help message and exit

       --limit N
              How  many  candidate regions (contig or transcript) to consider per BUSCO (default:

              Print the list of available BUSCO datasets

       --long Optimization Augustus self-training mode (Default: Off); adds considerably  to  the
              run time, but can improve results for some non-model organisms

       --metaeuk_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
              Pass  additional  arguments  to  Metaeuk for the first run. All arguments should be
              contained within a single pair of quotation marks, separated by commas.

       --metaeuk_rerun_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
              Pass additional arguments to Metaeuk for the second run. All  arguments  should  be
              contained within a single pair of quotation marks, separated by commas.

              To indicate that BUSCO cannot attempt to download files

       --out_path OUTPUT_PATH
              Optional  location  for  results  folder, excluding results folder name. Default is
              current working directory.

       -q, --quiet
              Disable the info logs, displays only errors

       -r, --restart
              Continue a run that had already partially completed.

       --tar  Compress some subdirectories with many files to save space

              Download and replace with last versions all lineages datasets and  files  necessary
              to their automated selection

       -v, --version
              Show this version and exit


        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.