Adding Hisat2 instead of BWA

Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.

GNU General Public License v3.0

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Adding Hisat2 instead of BWA #109

Closed arslan9732 closed 1 year ago

arslan9732 commented 1 year ago

Hi, Is it possible to incorporate hisat2 with flag --no-spliced-alignment instead of bwa inside NextPolish? Because hisat2 is faster enough as compared to bwa.

moold commented 1 year ago

Hi, you can also use your own alignment pipeline, see here. In this case you can use any mapping tools.