This App runs Minimap2 (version 2.10) to:
index a reference genome for use with Minimap2
Minimap2 requires the following:
- reference genome in fasta format (may be gzipped)
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> minimap2
- Reference genome fasta file
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.
When run with the test data and parameters you should get the following files:
- 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.
- This is the alignment file generated by the app. It is in PAF format.