adam
bdg-formats
| adam | bdg-formats | |
|---|---|---|
| 3 | 1 | |
| 967 | 38 | |
| 0.2% | - | |
| 6.1 | 5.4 | |
| about 1 month ago | 4 months ago | |
| Scala | Shell | |
| Apache License 2.0 | Apache License 2.0 |
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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
bdg-formats
-
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
What are some alternatives?
seq - A high-performance, Pythonic language for bioinformatics
asdf - ASDF (Advanced Scientific Data Format) is a next generation interchange format for scientific data
bioconda-recipes - Conda recipes for the bioconda channel.
nimconf2021 - Slides for Nimconf21
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
asdf - Extendable version manager with support for Ruby, Node.js, Elixir, Erlang & more
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)