Seq: A programming language for high-performance computational genomics

• seq

  15 634 0.7 C++

  Discontinued A high-performance, Pythonic language for bioinformatics

  

They support both, and will deprecate Python 2 style soon.

https://github.com/seq-lang/seq/issues/223

• bioconda-recipes

  5 1,565 10.0 Shell

  Conda recipes for the bioconda channel.

  

Seems like there's a conda packaging on the works: https://github.com/bioconda/bioconda-recipes/pull/29660

• InfluxDB

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• nimconf2021

  1 5 1.8 HTML

  Slides for Nimconf21

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.

• Nim

  346 16,060 9.9 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).

  

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

  1 2 0.0

  Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang

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

• Biopython

  31 4,158 9.6 Python

  Official git repository for Biopython (originally converted from CVS)

  

It might be pretty useful as a teaching tool, but I'm skeptical of its long-term benefit to professionals. I'm not sure the ecosystem of Seq users will be large enough, y'know? Again, it's pretty impressive work, and it's come a long way. I wish the devs all the best. :)

1. https://biopython.org/

• adam

  3 967 6.1 Scala

  ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

  

We're here, still plugging along.

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

https://github.com/bigdatagenomics/adam

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