<jellyProtocol>
    <reference>/__PATH__/_TO_/jellyExample/data/reference/lambda.fasta</reference>  
    <outputDir>/__PATH__/_TO_/jellyExample/</outputDir>
    <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 4 -noSplitSubreads</blasr>
    <input baseDir="/__PATH__/_TO_/jellyExample/data/reads/">
        <job>filtered_subreads.fastq</job>
    </input>
</jellyProtocol>
