Workflows

Genome assembly workflow for nanopore reads, for TSI

Input:

• Nanopore reads (can be in format: fastq, fastq.gz, fastqsanger, or fastqsanger.gz)

Optional settings to specify when the workflow is run:

• [1] how many input files to split the original input into (to speed up the workflow). default = 0. example: set to 2000 to split a 60 GB read file into 2000 files of ~ 30 MB.
• [2] filtering: min average read quality score. default = 10
• [3] filtering: min read length. default = 200
• [4] ...

Assembly with Flye; can run alone or as part of a combined workflow for large genome assembly.

• What it does: Assembles long reads with the tool Flye
• Inputs: long reads (may be raw, or filtered, and/or corrected); fastq.gz format
• Outputs: Flye assembly fasta; Fasta stats on assembly.fasta; Assembly graph image from Bandage; Bar chart of contig sizes; Quast reports of genome assembly
• Tools used: Flye, Fasta statistics, Bandage, Bar chart, Quast
• Input parameters: None required, but recommend ...