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.

busco 5.2.2                                         July 2021                                           BUSCO(1)