minimap2

Minimap2 is a sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads (or their assemblies) to a reference genome. This program works efficiently with query sequences ranging from a few kilobases to ~100 megabases with an error rate ~15%. Outputs to either PAF or SAM file formats.

Can multithread with the following limitations. It uses at most 3 threads when indexing target sequences. When mapping reads it can use N+1 threads, where the extra thread is used for IO operations.

Parallel Capabilities: Single core default, Multithreading options supported.