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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Graphmap owler 0.5.2

This App runs Graphmap (version 0.5.2):

A highly sensitive and accurate mapper for long, error-prone reads

App Creator

Amanda Cooksey

Quick Start

Graphmap requires the following:
  • reference genome in fasta format (may be gzipped)  (an index (.owlidx) of the reference genome may be provided as well if one has already been generated)
  • 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 -> Graphmap

 

Input File(s)

  • Reference genome fasta file
    • GCF_000240185.1_ASM24018v2_genomic.fna
  • Oxford Nanopore reads file
    • fastq_runid_01f68662d08b0a5d21077bf590c4c497b9092ef0_0.fastq

Parameters Used in App

  • In the Input section choose the reference genome fasta input file: 'GCF_000146045.2_R64_genomic.fna.gz'.
  • In the Input section select the Oxford Nanopore reads input file: 'fastq_runid_01f68662d08b0a5d21077bf590c4c497b9092ef0_0.fastq'. 
  • In the Output section name the output file 'testout.paf'
  • In the Output section select PAF as the output format
  • All remaining parameters may be left as default. 

Output File(s)

  • GCF_000146045.2_R64_genomic.fna.gmidx
    • 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. Following the above parameters it will be named 'testout.paf.

Tool Source for App

https://github.com/isovic/graphmap

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