nimconf2021
seq-genomics
| nimconf2021 | seq-genomics | |
|---|---|---|
| 1 | 1 | |
| 5 | 2 | |
| - | - | |
| 1.8 | 0.0 | |
| over 2 years ago | about 4 years ago | |
| HTML | ||
| - | - |
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nimconf2021
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Seq: A programming language for high-performance computational genomics
Nim has had some success in genomics mainly thanks to the work of https://github.com/brentp
Nim can be sold as a "A strongly-typed and statically-compiled high-performance Pythonic language" as Seq (although it is more than that and does not actually have as a goal to be Pythonic, see https://nim-lang.org/ or https://github.com/Araq/nimconf2021/blob/main/zennim.rst).
Still, given the small size of Nim community and even smaller size of the genomics nim subcommunity, I would say it is not that odd that is not included in the benchmark. The existing nim genomics library might not even cover the functionalities requested by the benchmark.
seq-genomics
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Seq: A programming language for high-performance computational genomics
Used it for coding Coursera/Stepik's Bioinformatics course [1] when it was first announced 2 years ago.
Not claiming it as any sort of reference, but you can see how it [2] may be used to solve some basic genome sequencing.
[1] https://www.coursera.org/specializations/bioinformatics
[2] https://github.com/fuzzthink/seq-genomics
What are some alternatives?
bioconda-recipes - Conda recipes for the bioconda channel.
seq - A high-performance, Pythonic language for bioinformatics
adam - ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Nim - Nim is a statically typed compiled systems programming language. It combines successful concepts from mature languages like Python, Ada and Modula. Its design focuses on efficiency, expressiveness, and elegance (in that order of priority).
Biopython - Official git repository for Biopython (originally converted from CVS)