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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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do wrong parameters on -x sequencing technologies affect on alignment results? #81

Closed holiday10 closed 4 years ago

holiday10 commented 4 years ago

i use the -x pacbio on nanopore reads alignment, but still get a bam file, does it affect the SV calling and analysis?

fritzsedlazeck commented 4 years ago

It can be. There are different optimizations to better cope with the error characteristics of the two sequencing technologies.