NAME

       flye - Assembly of long reads with repeat graphs

SYNAPSIS

       flye   (--pacbio-raw  |  --pacbio-corr  |  --pacbio-hifi  |  --nano-raw  |  --nano-corr  |
       --subassemblies) file1 [file_2 ...]  --genome-size SIZE --out-dir PATH

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

DESCRIPTION

       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.

       You must provide an estimate of the genome size as input, which is used for  solid  k-mers
       selection.  Standard  size  modifiers  are  supported  (e.g.  5m  or 2.6g). In the case of
       metagenome assembly, the expected total assembly size should be provided.

       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 option.
       Typically, 40x coverage is enough to produce good disjointigs.

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

OPTIONS

   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]

       --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

AUTHOR

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