NAME

       busco - benchmarking sets of universal single-copy orthologs

DESCRIPTION

       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
       https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO

   optional arguments:
       -i SEQUENCE_FILE, --in SEQUENCE_FILE
              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.

       --augustus
              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.

       --auto-lineage
              Run auto-lineage to find optimum lineage path

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

       --auto-lineage-prok
              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:
              3)

       --list-datasets
              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.

       --offline
              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

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

       -v, --version
              Show this version and exit

AUTHOR

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