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bede / hostile

Precise host read removal
MIT License
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Bowtie2 performance suffers when using many threads in some conditions #21

Closed bede closed 1 year ago

bede commented 1 year ago

For some datasets, Bowtie2's CPU utilisation decreases with increasing numbers of threads. Workaround is not to use more than 8-16 threads. Raised upstream https://github.com/BenLangmead/bowtie2/issues/437

bede commented 1 year ago

Considering pinning bowtie2=2.4.4 in next release as per https://github.com/BenLangmead/bowtie2/issues/437#issuecomment-1647082173

bede commented 1 year ago

bowtie2=2.4.5 also works https://github.com/BenLangmead/bowtie2/issues/437#issuecomment-1651708352

bede commented 1 year ago

Fixed upstream https://github.com/BenLangmead/bowtie2/issues/437