swarm
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torognes
A robust and fast clustering method for amplicon-based studies
Header length used to be limited to 2,048 characters. There is no specific limit imposed on header lengths anymore. Yet, a long header can trigger a segmentation fault on my...
Roadmap
For complete transparency, this is the roadmap I have in mind for swarm. Of course, this is completely open for discussion. > Semantic Versioning 2.0.0 > > Given a version...
Adapt SWARM to [AVX2](https://en.wikipedia.org/wiki/Advanced_Vector_Extensions#Advanced_Vector_Extensions_2) and the 256-bit registers available in the new Intel Haswell CPUs that became available in June 2013. Should allow 32-way SIMD parallellisation.
[Qiime 2](http://2.qiime.org/) now offers an interface for third-party plugins. The [plugin creation](https://docs.qiime2.org/2017.2/plugins/developing/) does not seem complicated: the plugin is a python 3 wrapper presenting some or all the functionalities of...
A user have suggested an option to exclude seeds sequences or clusters with low abundance (e.g. singletons). This could be applied to the dereplicated input sequences or to the output...
The Bloom filter code should be refactored. The bloompat code can be removed. The bloomflex code could also be made even more flexible by allowing the number of patterns to...
Hi all, I was wandering how SWARM (v2 or v3) is dealing with the new Binned Quality score from Illumina (https://www.illumina.com/documents/products/technotes/technote_understanding_quality_scores.pdf). I did not see anything in the official documentation,...
Running tests on ARM64 for the `dev` branch would be nice. Debug compilation with the latest GCC and clang (Ubuntu LTS 24.04), pull tests from `frederic-mahe/swarm-tests`. @lczech can help!