adam
sito
| adam | sito | |
|---|---|---|
| 3 | 2 | |
| 967 | 0 | |
| 0.2% | - | |
| 6.1 | 0.0 | |
| about 1 month ago | over 1 year ago | |
| Scala | Python | |
| Apache License 2.0 | MIT License |
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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
sito
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Ask HN: What's your favorite programmer niche?
As of recent I've been weirdly fascinated with codecs, serialization protocols, file formats, and the like. It scratches that low-level hacking itch (I spent most of my professional programming in web dev space) without as much commitment to electronics (used to be super big into arduino but I find that's harder to pick up and put down).
I've started hacking on my own container format (yeah, I know, xkcd927), after finding it super frustrating to embed arbitrary time-synched data streams into mp4/matroska/ogg/etc. Also it bugs me how crusty, complicated, and arcane mp4 is, and at the same time, mastroska and ogg are weirdly opaque given how they are supposed to be open standards.
If anyone is curious, here's my container format I've been developing: https://github.com/xkortex/sito
- Advanced Scientific Data Format
What are some alternatives?
seq - A high-performance, Pythonic language for bioinformatics
asdf - Extendable version manager with support for Ruby, Node.js, Elixir, Erlang & more
bioconda-recipes - Conda recipes for the bioconda channel.
uvfs - Microscopic C++20 archive format
nimconf2021 - Slides for Nimconf21
asdf - ASDF (Advanced Scientific Data Format) is a next generation interchange format for scientific data
notesutils - Utilities for extracting notes from Notes.app. This repository is lightly maintained and mainly exists to serve as documentation and starting point for your own scripts.
cramino - A *fast* tool for BAM/CRAM quality evaluation, intended for long reads
mleap - MLeap: Deploy ML Pipelines to Production