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**Note: [minimap2][minimap2] has replaced BWA-MEM for PacBio and Nanopore read **Note: [minimap2][minimap2] has replaced BWA-MEM for PacBio and Nanopore read
alignment.** It is ~50 times as fast, more accurate, produces better base-level alignment.** It is ~50 times as fast, more accurate, produces better base-level
alignment and works with long RNA-seq reads and long-read assemblies. alignment and works with long RNA-seq reads and long-read assemblies.
[minimap2]: https://github.com/lh3/minimap2 [minimap2]: https://github.com/lh3/minimap2
## Getting started ## Getting started