About the aligner? - Githubissues

mobinasri / secphase

Phasing reads with secondary alignments

MIT License

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About the aligner? #12

Open GRGong opened 8 months ago

GRGong commented 8 months ago

Hi,

Thanks for the magic tool!

I recently learned that secphase is used in PHARAOH.wdl for phasing HiFi reads. I'm wondering if there is a suggested aligner to generate related files like "allHifiToDiploidBam", "allONTToHap1Bam" and "hap2_to_hap1.paf". minimap2 or winnowmap?

Best, Gaorui