It might be much faster to use one massive, crazy sed call than to have python parse it out at the BAM stage, even with cythonization. Give it a shot when we have time.
It currently takes ~30 minutes to process a full MiSeq run, including alignment, sed, and tagging. Is that unacceptable?
dnbaker
commented
9 years ago
It might be much faster to use one massive, crazy sed call than to have python parse it out at the BAM stage, even with cythonization. Give it a shot when we have time.
It currently takes ~30 minutes to process a full MiSeq run, including alignment, sed, and tagging. Is that unacceptable?