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Daniel-Liu-c0deb0t / UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
MIT License
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parallelization ? #16

Open karlkashofer opened 2 years ago

karlkashofer commented 2 years ago

Hi ! I am looking for ways to parallelize umicollapse. What does -t: parallelize the deduplication of each separate alignment position. Using this is discouraged as it is lacking many features. mean ? What features are missing ? thanks, KK

Daniel-Liu-c0deb0t commented 2 years ago

If I recall correctly, parallelization with -t only works with single-end reads and with the sam/bam modes.

Also I don't think I observed a large performance increase from parallelism.