The compatibility with lra aligner

friend1ws / nanomonsv

SV detection tool for nanopore sequence reads

GNU General Public License v3.0

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The compatibility with lra aligner #8

Closed charliechen912ilovbash closed 3 years ago

charliechen912ilovbash commented 3 years ago

Hi,

Recently I am wondering about the compatibility between NanomonSV and lately released aligner lra: https://www.biorxiv.org/content/10.1101/2020.11.15.383273v1.full https://github.com/ChaissonLab/LRA Is it better than minimap2-NanomonSV combination?

Charlie

friend1ws commented 3 years ago

I have not performed yet. I'm aware that nanomonsv + minimap2 and nanomonsv + NGMLR work fine. I may do experiments (I'm also interested in trying Winnowmap). But I greatly welcome your feedback when you try it.

waltergallegog commented 2 years ago

Hi, Did you guys try to use LRA+nanomonsv? I'm getting an error in the parsing step, almost immediately after issuing the command:

06/20/2022 19:03:50 - nanomonsv.parse - ERROR - query end inconsistent!! 9b26abd9-75df-423f-bcd7-806e852e34c5: 31627 != 2246

real    0m0.403s
user    0m0.335s
sys     0m0.066s