Program options for flye: 

usage: flye (--pacbio-raw | --pacbio-corr | --pacbio-hifi | --nano-raw |
	     --nano-corr | --subassemblies) file1 [file_2 ...]
	     --out-dir PATH

	     [--genome-size SIZE] [--threads int] [--iterations int]
	     [--meta] [--plasmids] [--trestle] [--polish-target]
	     [--keep-haplotypes] [--debug] [--version] [--help] 
	     [--resume] [--resume-from] [--stop-after] 
	     [--hifi-error] [--min-overlap SIZE]

Assembly of long reads with repeat graphs

optional arguments:
  -h, --help            show this help message and exit
  --pacbio-raw path [path ...]
                        PacBio raw reads
  --pacbio-corr path [path ...]
                        PacBio corrected reads
  --pacbio-hifi path [path ...]
                        PacBio HiFi reads
  --nano-raw path [path ...]
                        ONT raw reads
  --nano-corr path [path ...]
                        ONT corrected reads
  --subassemblies path [path ...]
                        high-quality contigs input
  -g size, --genome-size size
                        estimated genome size (for example, 5m or 2.6g)
  -o path, --out-dir path
                        Output directory
  -t int, --threads int
                        number of parallel threads [1]
  -i int, --iterations int
                        number of polishing iterations [1]
  -m int, --min-overlap int
                        minimum overlap between reads [auto]
  --asm-coverage int    reduced coverage for initial disjointig assembly [not
                        set]
  --hifi-error float    expected HiFi reads error rate (e.g. 0.01 or 0.001)
                        [0.01]
  --plasmids            rescue short unassembled plasmids
  --meta                metagenome / uneven coverage mode
  --keep-haplotypes     do not collapse alternative haplotypes
  --trestle             enable Trestle [disabled]
  --polish-target path  run polisher on the target sequence
  --resume              resume from the last completed stage
  --resume-from stage_name
                        resume from a custom stage
  --stop-after stage_name
                        stop after the specified stage completed
  --debug               enable debug output
  -v, --version         show program's version number and exit

Input reads can be in FASTA or FASTQ format, uncompressed
or compressed with gz. Currently, PacBio (raw, corrected, HiFi)
and ONT reads (raw, corrected) are supported. Expected error rates are
<30% for raw, <3% for corrected, and <1% for HiFi. Note that Flye
was primarily developed to run on raw reads. Additionally, the
--subassemblies option performs a consensus assembly of multiple
sets of high-quality contigs. You may specify multiple
files with reads (separated by spaces). Mixing different read
types is not yet supported. The --meta option enables the mode
for metagenome/uneven coverage assembly.

Genome size estimate is no longer a required option. You
need to provide an estimate if using --asm-coverage option.

To reduce memory consumption for large genome assemblies,
you can use a subset of the longest reads for initial disjointig
assembly by specifying --asm-coverage and --genome-size options. Typically,
40x coverage is enough to produce good disjointigs.

You can run Flye polisher as a standalone tool using
--polish-target option.


----------------------------------------------