Alignment of ONT data in a Java program through processBuilder

[PMue]

I have a Java-based program for alignment and variant calling. So far we have been using only illumina reads and relied on Bowtie2, which generated great alignments and everything worked out just fine. I have implemented the Bowtie 2 pipeline, using the processBuilder in Java and the bowtie2.exe file.

I want to implement ONT alignments now and tried a Minimap2 impementation, however there is so .exe whatsoever in the downloaded file.

Does one of you have an idea if its easily possible to implement the minimap2 command in a processBuilder or is any other ONT alignment program is maybe more suitable for such kind of operation ?

Thanks

[GenomicSeq]

Hey PMue

I'm pretty sure it's possible to use Minimap2 for ONT read alignment in Java using the ProcessBuilder class. You just need to download the Minimap2 binary executable for your operating system from the Minimap2 GitHub repository and ensure that it is in your system's PATH environment variable so that it can be executed from the command line.

Once you have Minimap2 installed and set up, you can use the ProcessBuilder class to execute it and pass in the necessary command-line arguments. I think something like this.

ProcessBuilder pb = new ProcessBuilder("minimap2", "-ax", "map-ont", "reference.fasta", "reads.fastq");
pb.redirectOutput(new File("aligned.sam"));
Process p = pb.start();
p.waitFor();

This code should run Minimap2 with the "map-ont" preset, aligning the ONT reads in the "reads.fastq" file to the reference genome in "reference.fasta", and outputting the resulting SAM alignment file to "aligned.sam".

Also, I think you can customize the Minimap2 command-line options by modifying the arguments passed to ProcessBuilder. But there are other ONT read aligners that you might consider using include NGMLR, GraphMap, and LAST.

If this doesn't work then let me know and I'll try to work out something else.