nimconf2021
adam
nimconf2021 | adam | |
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1 | 3 | |
5 | 967 | |
- | 0.2% | |
1.8 | 6.1 | |
over 2 years ago | about 1 month ago | |
HTML | Scala | |
- | Apache License 2.0 |
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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.
adam
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biobear -- python package with minimal dependencies for bioinformatic file parsing and querying using rust and polars as the backend
FYI: ADAM seems to do that
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Advanced Scientific Data Format
We presented using Parquet formats for bioinformatics 2012/13-ish at the Bioinformatics Open Source Conference (BOSC) and got laughed out of the place.
While using Apache Spark for bioinformatics [0] never really took off, I still think Parquet formats for bioinformatics [1] is a good idea, especially with DuckDB, Apache Arrow, etc. supporting Parquet out of the box.
0 - https://github.com/bigdatagenomics/adam
1 - https://github.com/bigdatagenomics/bdg-formats
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Seq: A programming language for high-performance computational genomics
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
What are some alternatives?
bioconda-recipes - Conda recipes for the bioconda channel.
seq - A high-performance, Pythonic language for bioinformatics
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).
asdf - ASDF (Advanced Scientific Data Format) is a next generation interchange format for scientific data
Biopython - Official git repository for Biopython (originally converted from CVS)
cramino - A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
seq-genomics - Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang
uvfs - Microscopic C++20 archive format
sito - sito: A serialization suite
mleap - MLeap: Deploy ML Pipelines to Production