seq-genomics
adam
| seq-genomics | adam | |
|---|---|---|
| 1 | 3 | |
| 2 | 967 | |
| - | 0.2% | |
| 0.0 | 6.1 | |
| about 4 years ago | about 1 month ago | |
| Scala | ||
| - | Apache License 2.0 |
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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
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?
seq - A high-performance, Pythonic language for bioinformatics
bioconda-recipes - Conda recipes for the bioconda channel.
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).
nimconf2021 - Slides for Nimconf21
asdf - ASDF (Advanced Scientific Data Format) is a next generation interchange format for scientific data
cramino - A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
uvfs - Microscopic C++20 archive format
sito - sito: A serialization suite
mleap - MLeap: Deploy ML Pipelines to Production