Grabseqs

#to grab sequences for a SRA project ID, using 24 threads and saving data and metadata
# the -o option will create the directory if it doesn't already exist
grabseqs sra -t 24 -m metadata.csv -o proj/ -r 3 PRJN#######

usage: grabseqs [-h] [--version] {sra,imicrobe,mgrast} ...

Download metagenomic sequences from public datasets.

positional arguments:
  {sra,imicrobe,mgrast}
                        repositories available
    sra                 download from SRA
    imicrobe            download from iMicrobe
    mgrast              download from MG-RAST

optional arguments:
  -h, --help        show this help message and exit
  -m METADATA       filename in which to save SRA metadata (.csv format,
                    relative to OUTDIR)
  -o OUTDIR         directory in which to save output. created if it doesn't
                    exist
  -r RETRIES        number of times to retry download
  -t THREADS        threads to use (for fasterq-dump/pigz)
  -f                force re-download of files
  -l                list (but do not download) samples to be grabbed
  --parse_run_ids   parse SRR/ERR identifers (do not pass straight to fasterq-
                    dump)
  --custom_fqdump_args CUSTOM_FQD_ARGS
                    "string" containing args to pass to fastq-dump
  --use_fastq_dump  use legacy fastq-dump instead of fasterq-dump (no
                    multithreaded downloading)