NAME

       nad - download genome files from NCBI by accession

SYNOPSIS

       nad [-h] [-m {nucleotide,protein}] [-e {none,loads,all}]

DESCRIPTION

       Script to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.

OPTIONS

       [-F   {fasta,genbank,featuretable,gff3}]   [-o   OUT]   [-p  PREFIX]  [-r]  [--url]  [-v]  NCBI-accession
       [NCBI-accession ...]

   positional arguments:
              NCBI-accession

   optional arguments:
       -h, --help
              show this help message and exit

       -m {nucleotide,protein}, --molecule {nucleotide,protein}
              Molecule type to download. Default: nucleotide

       -e {none,loads,all}, --extended-validation {none,loads,all}
              Perform extended validation. Possible options are 'none' to skip validation, 'loads' to  check  if
              the sequence file loads in Biopython, or 'all' to run all checks. Default: none

       -F {fasta,genbank,featuretable,gff3}, --format {fasta,genbank,featuretable,gff3}
              File format to download nucleotide sequences in.  Default: genbank

       -o OUT, --out OUT
              Single filename to use for the combined output.

       -p PREFIX, --prefix PREFIX
              Filename prefix to use for output files instead of using the NCBI ID.

       -r, --recursive
              Recursively get all entries of a WGS entry.

       --url  Instead of downloading the sequences, just print the URLs to stdout.

       -v, --verbose
              Print a progress indicator.

AUTHOR

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

nad 0.2.6                                           June 2020                                             NAD(1)