nimtorch
biofast
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nimtorch
- NimTorch: PyTorch front end by generating C++ native ATen code
- Nim Front End for Pytirch
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Why I Use Nim instead of Python for Data Processing
There’s been a tremendous amount of work optimizing blas _and_ ensuring it’s numerically stable. Julia made a good choice to use blas first. Though it’s good to see new native implementations.
For Nim, there’s also NimTorch which is interesting in that it builds on Nim’s C++ target to generate native PyTorch code. Even Python is technically a second class citizen for the C++ code. Most ML libraries are C++ all the way down.
https://github.com/sinkingsugar/nimtorch
biofast
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Parsing huge files in Python
FYI: the python packages I mentioned earlier can all directly read gzip'd fastq files. See also this repo for examples.
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Does Rust Support Reading in FATSA files?
needletail is rated in the Heng Li benchmark (https://github.com/lh3/biofast/)
- Why I Use Nim instead of Python for Data Processing
What are some alternatives?
Arraymancer - A fast, ergonomic and portable tensor library in Nim with a deep learning focus for CPU, GPU and embedded devices via OpenMP, Cuda and OpenCL backends
scikit-bio - scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
PrimesResult - The results of the Dave Plummer's Primes Drag Race
readfq - Fast multi-line FASTA/Q reader in several programming languages
viroiddb - A curated database of all available viroid-like RNA sequences
nimpy - Nim - Python bridge
RecursiveFactorization.jl
nimpylib - Some python standard library functions ported to Nim
benchmarks - Some benchmarks of different languages