run.md

To run plassembler, first you need to install the database in a directory of your chosing:

plassembler download -d <database directory>

Once this is finished, you can run Plassembler as follows:

plassembler run -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated lower bound of chromosome length>

• -c or --chromosome will default to 1000000 if not specified.

To specify more threads to speed up Plassembler, use -t or --threads:

plassembler run -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated chromosome length> -t <threads>

plassembler defaults to 1 thread.

To specify a prefix for the output files, use -p or --prefix:

plassembler run -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated chromosome length> -t <threads> -p <prefix>

To specify a minimum length and minimum read quality Q-score for chopper, use -m and -q :

plassembler run -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated chromosome length> -t <threads> -p <prefix> -m <min length> -q <min quality>

• -m will default to 500 and -q will default to 9.

To overwrite an existing output directory, use -f or --force

plassembler run -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated chromosome length> -t <threads>

To use Raven instead of Flye as a long read assembler, use --use_raven

plassembler run -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated chromosome length> -t <threads> --use_raven

To keep the Flye assembled chromosome(s) (as chromosome.fasta), use --keep-chromosome

plassembler run -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated chromosome length> -t <threads> --keep_chromosome

To use pacbio reads use --pacbio_model (e.g. with regular CLR reads so with pacbio-raw model specified in Flye):

plassembler run -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated chromosome length> -t <threads> --pacbio_model pacbio-raw

To skip quality control (chopper and fastp), use --skip_qc

plassembler run -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated chromosome length> -t <threads> --skip_qc

To use assembled mode to calculate plasmid copy numbers, you need to use plassembler assembled, along with an already assembled chromosome with --input_chromosome and plasmids with --input_plasmids.

plassembler assembled -d <database directory> -l <long read fastq> -o <output dir> -1 < short read R1 fastq> -2 < short read R2 fastq> -c <estimated chromosome length> -t <threads> -a --input_chromosome <path to chromosome FASTA> --input_plasmids <path to plasmids FASTA>

You can also use plassembler long, which will simply run Flye and keep all contigs below -c and denote them as 'plasmids', but this is experimental only for now and I do not vouch for its performance.

Usage: plassembler run [OPTIONS]

  Runs Plassembler

Options:
  -h, --help                Show this message and exit.
  -V, --version             Show the version and exit.
  -d, --database PATH       Directory of PLSDB database.  [required]
  -l, --longreads PATH      FASTQ file of long reads.  [required]
  -1, --short_one PATH      R1 short read FASTQ file.  [required]
  -2, --short_two PATH      R2 short read FASTQ file.  [required]
  -c, --chromosome INTEGER  Approximate lower-bound chromosome length of
                            bacteria (in base pairs).  [default: 1000000]
  -o, --outdir PATH         Directory to write the output to.  [default:
                            plassembler.output/]
  -m, --min_length TEXT     minimum length for filtering long reads with
                            chopper.  [default: 500]
  -q, --min_quality TEXT    minimum quality q-score for filtering long reads
                            with chopper.  [default: 9]
  -t, --threads TEXT        Number of threads.  [default: 1]
  -f, --force               Force overwrites the output directory.
  -p, --prefix TEXT         Prefix for output files. This is not required.
                            [default: plassembler]
  --skip_qc                 Skips qc (chopper and fastp).
  --pacbio_model TEXT       Pacbio model for Flye.  Must be one of pacbio-raw,
                            pacbio-corr or pacbio-hifi.  Use pacbio-raw for
                            PacBio regular CLR reads (<20 percent error),
                            pacbio-corr for PacBio reads that were corrected
                            with other methods (<3 percent error) or pacbio-
                            hifi for PacBio HiFi reads (<1 percent error).
  -r, --raw_flag            Use --nano-raw for Flye.  Designed for Guppy fast
                            configuration reads.  By default, Flye will assume
                            SUP or HAC reads and use --nano-hq.
  --keep_fastqs             Whether you want to keep FASTQ files containing
                            putative plasmid reads  and long reads that map to
                            multiple contigs (plasmid and chromosome).
  --keep_chromosome         If you want to keep the chromosome assembly.
  --use_raven               Uses Raven instead of Flye for long read assembly.
                            May be useful if you want to reduce runtime.

All options

Usage: plassembler [OPTIONS] COMMAND [ARGS]...

Options:
  -h, --help     Show this message and exit.
  -V, --version  Show the version and exit.

Commands:
  assembled  Runs assembled mode
  citation   Print the citation(s) for this tool
  download   Downloads Plassembler DB
  long       Plassembler with long reads only - experimental and untested
  run        Runs Plassembler