Overview
Flye (citation) is a de novo assembler for long read data (e.g., Oxford Nanopore). It can be used in the assembling pipeline if the Ridom Typer client is running on Linux or if the Windows Subsystem for Linux is installed on Windows.
See the page long read de novo assembler evaluation for a detailed comparison of the performance.
Please note: It is a known issue that Flye sometimes may miss small plasmids or duplicate them.
Flye Assembling Options
The assembler options dialog in the pipeline script is used to specify the pre- and postprocessing, and to set additional Flye parameters.
- Read trimming with Chopper (citation)
- Read downsampling with Rasusa (citation) or Filtlong (citation)
- Assembly polishing with Medaka 2.0 (citation)
- ONT-cgMLST-Polisher
By default, the reads are trimmed with Chopper (quality 10, min length 500) and downsampled with Rasusa to 100x estimated coverage.
To read types are selectable in the settings dialog nano-hq for ONT data, and pacbio-hifi for PacBio HiFi data.
After assembling, medaka and ONT-cgMLST-Polisher are used by default to polish the assembly.
FOR RESEARCH USE ONLY. NOT FOR USE IN CLINICAL DIAGNOSTIC PROCEDURES.