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 index align 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 (.gmidx) 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)

Test Data


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 Input section select 'FASTQ' drop-down menu.
  • In the Output section name the output file 'testout.sam'
  • 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.sam'.

Tool Source for App

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