Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

• Speed and stability improvements for large datasets
• New option --polish-target to run Flye polisher on the target sequence

• Metagenome assembly support fully integrated (--meta option)
• New Trestle module for resolving simple unbridged repeats
• New --plasmids option that recovers short unassembled plasmids

• Installation instructions
• Usage

Flye is using repeat graph as a core data structure. In difference to de Bruijn graphs (which require exact k-mer matches), repeat graphs are built using approximate sequence matches, and can tolerate higher noise of SMS reads.

The edges of repeat graph represent genomic sequence, and nodes define the junctions. Each edges is classified into unique or repetitive. The genome traverses the graph (in an unknown way), so as each unique edge appears exactly once in this traversal. Repeat graphs reveal the repeat structure of the genome, which helps to reconstruct an optimal assembly.

Above is an example of the repeat graph of a bacterial assembly. Each edge is labeled with its id, length and coverage. Repetitive edges are shown in color, and unique edges are black. Note that each edge is represented in two copies: forward and reverse complement (marked with +/- signs), therefore the entire genome is represented in two copies. This is necessary because the orientation of input reads is unknown.

In this example, there are two unresolved repeats: (i) a red repeat of multiplicity two and length 35k and (ii) a green repeat cluster of multiplicity three and length 34k - 36k. As the repeats remained unresolved, there are no reads in the dataset that cover those repeats in full. Five unique edges will correspond to five contigs in the final assembly.

Repeat graphs produced by Flye could be visualized using AGB or Bandage.

The assemblies generated using Flye 2.4 could be downloaded from Zenodo

Flye package includes some third-party software:

• libcuckoo
• intervaltree
• lemon
• minimap2

Flye is distributed under a BSD license. See the LICENSE file for details.

Flye is developed in Pavel Pevzner's lab at UCSD

Code contributions:

• Repeat graph and current package maintaining: Mikhail Kolmogorov
• Trestle module and original polisher code: Jeffrey Yuan
• Original contig extension code: Yu Lin
• Short plasmids recovery module: Evgeny Polevikov

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs", bioRxiv, 2018 doi:10.1101/247148

Yu Lin, Jeffrey Yuan, Mikhail Kolmogorov, Max W Shen, Mark Chaisson and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using de Bruijn Graphs", PNAS, 2016 doi:10.1073/pnas.1604560113

Please report any problems to the issue tracker. If possible, please include "flye.log" file from the output directory for faster feedback. Alternatively, you can write directly to [email protected].