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.

flye 2.7.1                                          June 2020                                            FLYE(1)