mosdepth
nimpylib
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mosdepth
- Calculating Average Coverage or Read Depth for a Sequence (WES)
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Why is bedtools genomecov giving me a blank output file?
I'm not sure why that happens, but an alternative to bedtools genomecov is mosdepth. Maybe you can try that tool instead as it's very reliable.
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Is there a tool that quantifies “spatial coverage”, that is what percentage of a reference assembly has a read mapped to it?
I would give mosdepth a look. It can provide depth across a chromosome/contig at each base, or a mean depth for a given window size (eg 1kb), or regions provided within a bed file, or a simple summary of the mean depth across each chromosome/contig.
nimpylib
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Why I Use Nim instead of Python for Data Processing
Another nim & python thread that has not been mentioned yet here
https://news.ycombinator.com/item?id=28506531 - project allows creating pythonic bindings for your nim libraries pretty easily, which can be useful if you still want to write most of your toplevel code in python, but leverage nim's speed when it matters.
If you want to make your nim code even more "pythonic" there is a https://github.com/Yardanico/nimpylib, and for calling some python code from nim there is a https://github.com/yglukhov/nimpy
What are some alternatives?
nimbus-eth1 - Nimbus: an Ethereum Execution Client for Resource-Restricted Devices
nimpy - Nim - Python bridge
nim-plotly - plotly wrapper for nim-lang
Primes - Prime Number Projects in C#/C++/Python
moe - A command line based editor inspired by Vim. Written in Nim.
scikit-bio - scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
INim - Interactive Nim Shell / REPL / Playground
boomer - Zoomer application for Linux
Unchained - A fully type safe, compile time only units library.
nim-playground-frontend - The front-end for https://play.nim-lang.org
adventofcode2022 - Advent of Code 2022 solutions in Nim
PrimesResult - The results of the Dave Plummer's Primes Drag Race