Alignment for ancient samples take a long time due to misincorporations from DNA damage and various contaminating sequences. Some environments may have a time limit for how long a task can run. Samples with a lot of reads could go over the limit, sometimes taking more than 72 hours to finish alignment. Although increasing the number of threads used for alignment can speed this up, very large samples can still take a long time. So a more scaleable solution is needed.
One solution is to split large fastqs into smaller chunks, align them in parallel and then merge them in the end before post-processing. In essence, artificially increasing the cores used to align the sample at the same time.
Alignment for ancient samples take a long time due to misincorporations from DNA damage and various contaminating sequences. Some environments may have a time limit for how long a task can run. Samples with a lot of reads could go over the limit, sometimes taking more than 72 hours to finish alignment. Although increasing the number of threads used for alignment can speed this up, very large samples can still take a long time. So a more scaleable solution is needed.
One solution is to split large fastqs into smaller chunks, align them in parallel and then merge them in the end before post-processing. In essence, artificially increasing the cores used to align the sample at the same time.