Minimap2_index-2.10
Minimap2_index-2.10
This App runs Minimap2 (version 2.10) to:
index a reference genome for use with Minimap2
App Creator
Amanda Cooksey
Quick Start
Minimap2 requires the following:
reference genome in fasta format (may be gzipped)
Resources
Test Data
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
Parameters Used in App
In the Input file section choose the reference genome fasta input file: 'GCF_000146045.2_R64_genomic.fna.gz'.
In the Index Parameters section select 'long-read spliced alignment' from the 'preset options' drop-down menu.
In the Output file section enter a file name (index.mmi) in the 'Dump index to FILE' field to save the index file generated by the app.
All remaining parameters may be left as default.
Output File(s)
When run with the test data and parameters you should get the following files:
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.