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bcgsc / RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads
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Release memory before redundancy reducing step. #40

Closed xiekunwhy closed 2 years ago

xiekunwhy commented 2 years ago

Hi,

Is it possible to run redundancy reducing step only or release memory usage before redundancy reducing step? Rna-bloom + Minimap2 may double the momery consuming.

Best, Kun

kmnip commented 2 years ago

Thanks for the suggestion. I will on improving this!

kmnip commented 2 years ago

Technically, RNA-Bloom isn't using much memory at the redundancy reduction step. The primary issue is that there are too many input sequences for minimap2.

I am testing an idea and I may incorporate it in the next release.

xiekunwhy commented 2 years ago

Hi @kmnip ,

Any progress?

Best regards, Kun

kmnip commented 2 years ago

Hi Kun, I will make a new release later this month. I will let you know. Thanks for your patience! Ka Ming

kmnip commented 2 years ago

@xiekunwhy Sorry for the delays... This issue is fixed now. Please see my new release of RNA-Bloom v2.0.0: https://github.com/bcgsc/RNA-Bloom/releases/tag/v2.0.0