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NVIDIA-Genomics-Research / GenomeWorks

SDK for GPU accelerated genome assembly and analysis
https://clara-parabricks.github.io/GenomeWorks/
Apache License 2.0
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[cudapoa][cudaaligner] adding support for different types of gap penalty #496

Open r-mafi opened 4 years ago

r-mafi commented 4 years ago

The current implementation supports constant gap penalty. This issue suggests adding linear, affine and convex types as well.

r-mafi commented 4 years ago

e.g. the following input

>s0
AAAAAAAAAAAAAAAAAAAAAA
>s1
AAAAAAAAAAAAAAAAAAAAAA
>s2
AAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTT

generates the following consensus:

AAAAAAAAAAAAAAAAAAAAAATTTTTTTTTTT

@tijyojwad , @atadkase