seq
adam
Our great sponsors
seq | adam | |
---|---|---|
15 | 3 | |
634 | 967 | |
- | 0.1% | |
0.7 | 6.1 | |
over 1 year ago | about 1 month ago | |
C++ | Scala | |
Apache License 2.0 | Apache License 2.0 |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
seq
- Bioinformatics programming language
-
A Python-based programming language for high-performance computational genomics
> Seq is a Python-compatible language, and the vast majority of Python programs should work without any modifications
https://github.com/seq-lang/seq
- Seq – A programming language for computational genomics and bioinformatics
-
Hacker News top posts: Sep 15, 2021
Seq: A programming language for high-performance computational genomics\ (17 comments)
-
Seq: A programming language for high-performance computational genomics
They support both, and will deprecate Python 2 style soon.
https://github.com/seq-lang/seq/issues/223
adam
-
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
-
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
-
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?
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).
bioconda-recipes - Conda recipes for the bioconda channel.
edlib - Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
nimconf2021 - Slides for Nimconf21
wyng-backup - Fast Time Machine-like backups for logical volumes & disk images
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
bowtie2 - A fast and sensitive gapped read aligner
uvfs - Microscopic C++20 archive format
seq-genomics - Coursera Bioinformatics / Stepik Genome Sequencing with seq-lang
sito - sito: A serialization suite