search

raja-appuswamy / accel-align-release

A fast seed-embed-extend based sequence mapper and aligner
MIT License
22 stars 6 forks source link

embedding question #18

Closed fmughal closed 2 years ago

fmughal commented 2 years ago

Hello Raja,

Is there an option to disable embedding in accel-align (similar to the demonstration in the publication) or would that require changes to the source code prior to compilation?

Thanks, -Fizza

yanlolo commented 2 years ago

Hey Fizza,

Disable embedding will make the aligner super slow so we do not support an option to disable embedding publicly. We only did that to illustrate the impact of embedding. If you have a special requirement to used a mode without embedding, please let us know.

Regards, Yiqing

fmughal commented 2 years ago

Thank you, Yiqing. Yes, I'd like to try out accel-align without embedding (and of course, with embedding using the software out-of-the-box). The little bit of boost in accuracy at the cost of speed according to the accel-align paper, is of particular interest to me.

fmughal commented 2 years ago

Hello, I was hoping to follow up on my request for access to the accel-align no-embedding version. Thank you.

yanlolo commented 2 years ago

Hey Fizza,

I have added the option to disable embedding (extend all candidates) today. This mode could be enabled by '-d'. Please pull the last commit and try.

Example:

path-to-code/accel-align-release/accalign -l 32 -t $threads -d -o $output/accalign.sam \
    path-to-ref/hg37.fna $input/$r1
fmughal commented 2 years ago

Thank you, Yiqing!