Parallelize nanopolish eventalign
matthewstuartedwards opened this issue · 0 comments
matthewstuartedwards commented
Description of feature
The author of nanopolish has said that the recommended way to parallelize it is to split up the fastq files, then join the output files together.
nanoseq could operate on multiple fastq files in the input directory, and execute nanopolish event align in parallel.
I know xpore and m6anet operate using a single fastq file, so the input files will need to be concatenated for that step, but parallelizing nanopolish would speed up the overall operations of the pipeline.
Alternatively, if a single large fastq file is provided, nanoseq could split that file into chunks before running nanopolish event align.