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Add CHROMAP as aligner #233

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JoseEspinosa opened this issue Oct 26, 2021 · 4 comments
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Add CHROMAP as aligner #233

JoseEspinosa opened this issue Oct 26, 2021 · 4 comments
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feature-request Request to add new functionality
Milestone
2.0

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@JoseEspinosa
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From CHROMAP pre-print it is stated that chromap performs similarly in terms of accuracy to bwa while it is 10X faster. Might be interesting to enable it use.
@JoseEspinosa JoseEspinosa added this to the 2.0 milestone Oct 26, 2021
@drpatelh
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This would be awesome!! We could have a separate sub-workflow for this like we do with bwa_mem and add an --aligner option to select. I have been thinking it would be relatively easy to have a similar workflow for Bowtie2 as well for complete flexibility at the user-level (as mentioned in #160)

@JoseEspinosa JoseEspinosa mentioned this issue Oct 26, 2021
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@JoseEspinosa JoseEspinosa added feature-request Request to add new functionality and removed enhancement labels Oct 26, 2021
@JoseEspinosa
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I tried to implement chromap as an available aligner but found this issue haowenz/chromap#59 that should be fixed in v0.2.0, will need to update the module and try again.

@JoseEspinosa
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I open a PR on the BioContainers multi-package-containers repo, once the container is created I will bump the new version in the chromap module

@JoseEspinosa JoseEspinosa mentioned this issue Mar 30, 2022
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@JoseEspinosa
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Closed in #267

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@JoseEspinosa @drpatelh