Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.
Miniasm requires the following:
- a single fastq file of long reads
- a PAF file of all-vs-all read self-mappings
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Miniasm
- Fastq file of long reads:
- PAF file
Parameters Used in App
- Enter 'miniasm_out.gfa' in the 'output file name' field.
- Set the 'minimum span' to 200.
- All other options should remain as default.
Running the app with the above files and parameters results in a single output file: