Skip to main content

Flye

Flye is a de novo assembler for single-molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It currently supports FASTA and FASTQ files generated by PacBio and ONT technologies.

Input files are expected to have the following error rates and can either be compressed gz files or uncompressed:

  • less than 20% for PB CLR/regular ONT
  • less than 5% for ONT HQ
  • less than 3% for corrected
  • less than 1% for HiFi.

To load Flye on Palmetto 2 :

module load biocontainers
module load flye

To see an example of running this software please see their github page.

To get an explanation of their parameters please see their official documentation.

When a run is successful it will generate three files:

  • assembly.fasta which contains the Final assembly, along with contigs and possibly scaffolds
  • assembly_graph.gfa or .gv which contains the Final repeat graph.
  • assembly_info.txt which contains extra information about contigs (such as length or coverage)
tip

This software can use multiple threads try requesting a few extra cpu cores to speed it up! Don't forget the --threads= NUMBER OF CPU CORES flag though.

Parallel Capabilities : Multithreading options available.