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

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.

 

 

 

 

 

Skip to end of metadata
Go to start of metadata

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
Resources

Test Data

Icon

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

https://github.com/lh3/miniasm/blob/master/README.md

  • No labels