This App runs BWA mem (version 0.7.15) to
- Map long read sequencing data (such as Nanopore or PacBio) to a reference genome.
Sequencing files in FASTQ format. For paired-end data there should be two separate files (forward and reverse). For single-end data only the first file is required.
Reference genome sequence in FASTA format. You can either use a reference provided by CyVerse or provide your own file.
There are many optional parameters. However, default values are provided.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bwa_mem > longreads
Use 'SRR6364637_nano.fastq' as the left read file.
Use 'GCF_000686545.1_ASM68654v1_genomic.fna.gz' as the reference genome FASTA file
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the section below.
Check 'Nanopore data' under inputs.
This app, run with the parameters above, will generate 1 output file: bwa_output.sam.
The analysis folder will also contain the BWA index files made during your analysis.