.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH FLYE "1" "June 2020" "flye 2.7.1" "User Commands"
.SH NAME
flye \- Assembly of long reads with repeat graphs
.SH SYNAPSIS
.B flye
(\fB\-\-pacbio\-raw\fR | \fB\-\-pacbio\-corr\fR | \fB\-\-pacbio\-hifi\fR | \fB\-\-nano\-raw\fR |
\fB\-\-nano\-corr\fR | \fB\-\-subassemblies\fR) file1 [file_2 ...]
\fB\-\-genome\-size\fR SIZE \fB\-\-out\-dir\fR PATH
.IP
[\-\-threads int] [\-\-iterations int] [\-\-min\-overlap int]
[\-\-meta] [\-\-plasmids] [\-\-trestle] [\-\-polish\-target]
[\-\-keep\-haplotypes] [\-\-debug] [\-\-version] [\-\-help]
[\-\-resume] [\-\-resume\-from] [\-\-stop\-after]
.SH 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
\fB\-\-subassemblies\fR 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 \fB\-\-meta\fR option enables the mode
for metagenome/uneven coverage assembly.
.PP
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.
.PP
To reduce memory consumption for large genome assemblies,
you can use a subset of the longest reads for initial disjointig
assembly by specifying \fB\-\-asm\-coverage\fR option. Typically,
40x coverage is enough to produce good disjointigs.
.PP
You can run Flye polisher as a standalone tool using
\fB\-\-polish\-target\fR option.
.SH OPTIONS
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-pacbio\-raw\fR path [path ...]
PacBio raw reads
.TP
\fB\-\-pacbio\-corr\fR path [path ...]
PacBio corrected reads
.TP
\fB\-\-pacbio\-hifi\fR path [path ...]
PacBio HiFi reads
.TP
\fB\-\-nano\-raw\fR path [path ...]
ONT raw reads
.TP
\fB\-\-nano\-corr\fR path [path ...]
ONT corrected reads
.TP
\fB\-\-subassemblies\fR path [path ...]
high\-quality contigs input
.TP
\fB\-g\fR size, \fB\-\-genome\-size\fR size
estimated genome size (for example, 5m or 2.6g)
.TP
\fB\-o\fR path, \fB\-\-out\-dir\fR path
Output directory
.TP
\fB\-t\fR int, \fB\-\-threads\fR int
number of parallel threads [1]
.TP
\fB\-i\fR int, \fB\-\-iterations\fR int
number of polishing iterations [1]
.TP
\fB\-m\fR int, \fB\-\-min\-overlap\fR int
minimum overlap between reads [auto]
.TP
\fB\-\-asm\-coverage\fR int
reduced coverage for initial disjointig assembly [not
set]
.TP
\fB\-\-plasmids\fR
rescue short unassembled plasmids
.TP
\fB\-\-meta\fR
metagenome / uneven coverage mode
.TP
\fB\-\-keep\-haplotypes\fR
do not collapse alternative haplotypes
.TP
\fB\-\-trestle\fR
enable Trestle [disabled]
.TP
\fB\-\-polish\-target\fR path
run polisher on the target sequence
.TP
\fB\-\-resume\fR
resume from the last completed stage
.TP
\fB\-\-resume\-from\fR stage_name
resume from a custom stage
.TP
\fB\-\-stop\-after\fR stage_name
stop after the specified stage completed
.TP
\fB\-\-debug\fR
enable debug output
.TP
\fB\-v\fR, \fB\-\-version\fR
show program's version number and exit
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.