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 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)
Resources

Test Data

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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

Parameters Used in App

  • In the Input section choose the reference genome fasta input file: 'GCF_000146045.2_R64_genomic.fna.gz'.

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

Tool Source for App

https://github.com/isovic/graphmap

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