FLYE(1)

💖 FLYE(1) 💖

okay bestie, welcome to flye(1) — that's section 1 of the User Commands manual, and yes it's giving main character energy because this is the tool that assembles your long reads into actual genomes. sit down, grab a strawberry, we're doing this 🍓

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✨ NAME ✨

flye — assembly of long reads with repeat graphs. that's the whole vibe. that's the assignment. periodt. 👑

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🔥 SYNAPSIS 🔥

no cap, here's the exact invocation, copy it character for character:

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]

so you pick exactly one of those read-type flags, you hand it one or more files, and you must tell it the genome size and where to put the output. the square-bracket squad is optional, they're just there if you want them. 💅

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🌸 DESCRIPTION 🌸

okay so here's the tea. your input reads can be in FASTA or FASTQ format, and they can be uncompressed or compressed with gz — flye is not picky, she's flexible. 💁

right now, supported read types are PacBio (raw, corrected, HiFi) and ONT (raw, corrected). the expected error rates are:

• <30% for raw
• <3% for corrected
• <1% for HiFi

not me pointing out that Flye was primarily developed to run on raw reads — that's literally what the manpage says, so don't come for me. 🫶

also, the --subassemblies option does a consensus assembly of multiple sets of high-quality contigs — so if you already have good contigs and want them merged, that's your girl.

you can specify multiple files with reads, just separate them with spaces. but — and this is the important part — mixing different read types is not yet supported. pick a lane bestie. 😭

and if you're doing metagenomes, the --meta option turns on the mode for metagenome / uneven coverage assembly. slay. 🌈

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💫 the genome size thing (mandatory, sorry) 💫

you must provide an estimate of the genome size as input — it gets used for solid k-mers selection. standard size modifiers are supported, like 5m or 2.6g. no, you can't skip it, she needs the numbers. ✨

if you're doing metagenome assembly, you give the expected total assembly size instead. same vibe, different math. 🧚

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🦋 memory saving era 🦋

to reduce memory consumption for large genome assemblies, you can use a subset of the longest reads for the initial disjointig assembly by specifying the --asm-coverage option. typically, 40x coverage is enough to produce good disjointigs. that's it, that's the tip, no notes. 💜

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🎀 polisher as a standalone 🎀

you can run the Flye polisher as a standalone tool using the --polish-target option. she's independent, she's thriving, she doesn't need the whole pipeline. 👑

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✨ OPTIONS ✨

🌟 optional arguments: 🌟

one bullet per option, no skipping, we're thorough in this group chat:

• -h, --help — show this help message and exit. the classic. the goat. 🐐
• --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

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💜 AUTHOR 💜

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. respect the author bestie, they did that. 🫶

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and that's the whole page, no crumbs left. this was flye 2.7.1, dated June 2020, filed under FLYE(1) — ily, go assemble something iconic. 🎀💖✨