The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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Miniasm 0.2_r168

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. 

App Creator

Amanda Cooksey

Quick Start

Miniasm requires the following:
  • a single fastq file of long reads
  • a PAF file of all-vs-all read self-mappings

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Miniasm


Input File(s)

  • Fastq file of long reads:
    • concat_reads.fastq
  • PAF file 
    • minimap2_output.paf

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.

Output File(s)

Running the app with the above files and parameters results in a single output file:

  • miniasm_out.gfa

Tool Source for App

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