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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Minimap2_index_align-2.10

This App runs Minimap2 (version 2.10) to:

find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome.

App Creator

Amanda Cooksey

Quick Start

Minimap2 requires the following:
  • reference genome in fasta format (may be gzipped) or an index (.mmi) of the reference genome
  • long reads in fastq or fasta format (may be gzipped)
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 -> minimap2

 

Input File(s)

  • Reference genome fasta file
    • GCF_000146045.2_R64_genomic.fna.gz
  • Oxford Nanopore reads file
    • SRR6059712.fastq

Parameters Used in App

  • In the Index Parameters section choose the reference genome fasta input file: 'GCF_000146045.2_R64_genomic.fna.gz'.
  • In the Index Parameters section enter a file name (index.mmi) in the 'Dump index to FILE' field to save the index file created by the app.
  • In the Mapping and Alignment section select the Oxford Nanopore reads input file: 'SRR6059712.fastq'. 
  • In the Mapping and Alignment section select 'long-read spliced alignment' from the 'preset options' drop-down menu.
  • All remaining parameters may be left as default. 

Output File(s)

  • index.mmi
    • This is the index file of the genome generated by the app. This file may be used in future analyses in place of the reference genome fasta file.
  • output 
    • This is the alignment file generated by the app. It is in PAF format. 

Tool Source for App

https://github.com/lh3/minimap2

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