- To use Canu, input must be in fastq (PacBio) or fasta (Nanopore) format .
- Resources: https://canu.readthedocs.io/en/latest/quick-start.html
Use pacbio.fastq as PacBio fastq and oxford.fasta as Nanopore fasta input file.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- pacbio-raw: run correct, trim and assemble on PacBio raw reads
- pacbio-corrected: run trim and assemble on PacBio corrected reads
- nanopore-raw: run correct, trim and assemble on Oxford Nanopore raw reads
- nanopore-corrected: run trim and assemble on Oxford Nanopore corrected reads
- genome size can be represented in following format: 1m for 1Mbp, 1g for 1Gbp