FLYE

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.