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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


  • reference genome in fasta format (may be gzipped) or   (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)


  • 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