This App runs Minimap2 (version 2.10) to:
find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome.
Minimap2 requires the following:
- reference genome in fasta format (may be gzipped) or an index (.mmi) of the reference genome
- long reads in fastq or 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
- Oxford Nanopore reads file
Parameters Used in App
- In the Index Parameters section choose the reference genome fasta input file: 'GCF_000146045.2_R64_genomic.fna.gz'.
- In the Index Parameters section enter a file name (index.mmi) in the 'Dump index to FILE' field to save the index file created by the app.
- In the Mapping and Alignment section select the Oxford Nanopore reads input file: 'SRR6059712.fastq'.
- In the Mapping and Alignment section select 'long-read spliced alignment' from the 'preset options' drop-down menu.
- All remaining parameters may be left as default.
- 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.