Genome assembly with Flye
Assemble long reads with Flye, then view assembly statistics and assembly graph
- Author(s):
- Release: 0.2
- License: MIT
- UniqueID: 83ef6fdc-b8a9-41af-a824-0225f0199e63
Genome assembly with Flye workflow
Why use this workflow?
- This is a fairly simple workflow that assembles a genome from long sequencing reads.
- It takes in sequencing reads from PacBio (Hifi or non-Hifi), or Oxford Nanopore.
- If you have PacBio Hifi reads, you may prefer to use a workflow with the assembly tool Hifiasm, such as the those in the suite of VGP workflows.
Inputs
Raw sequencing reads from PacBio or Oxford Nanopore in format: fasta, fasta.gz, fastq, fastq.gz, fastqsanger.gz or fastqsanger
What does the workflow do
- Assembles the reads with the tool Flye
- Summarizes the statistics with the tool Fasta statistics
- Report with the tool Quast
- Renders the assembly graph with the tool Bandage
Settings
Run as-is or change parameters at runtime
For example:
- change the Flye option of "mode" to the correct sequencing type
- change the Quast option for "Type of organism" to correct taxon
Outputs
- Flye assembly output - four files: fasta, gfa for bandage, graph_dot file, assembly info
- Fasta statistics
- Bandage image
- Quast report