mosdepth
INim
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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.
INim
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Nim
- `nim secret`[0]: code is interpreted with Nim's vm, it is limited to compile-time (e.g. no C/C++).
- `nlvm r`[1]: nlvm backend supports JIT compilation and repl-like interface was added in latest release.
- `inim`[2]: supports all nim code, but it's not really a true repl. It adds code to a file and recompiles it (you can see the source file with `ctrl+x`). I'd recommend to use it with clang compiler, because it's a bit faster than gcc in my experience. It's the best option right now. And I use it almost daily.
First two options have rudimentary input system. But you can get command history and left-right navigation by wrapping them with rlwrap (should be preinstalled on most *nixes): `rlwrap nim secret`, `rlwrap nlvm r`.
There are plans to support incremental compilation for the next Nim release (it is currently broken). That would improve inim and other repls experience significantly.
[0]: https://nim-lang.org/docs/manual.html#restrictions-on-compil...
[1]: https://forum.nim-lang.org/t/10697
[2]: https://github.com/inim-repl/INim
- Could Nim be a complete replacement for Python?
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Writing a presentation to introduce rustlang to my dev team, and I've got to the "downsides" part.
Go must be terrible to google too! Nim's easy to google though, it's how I got to rust really. I'm actually the maintainer of inim, the nim repl: https://github.com/inim-repl/INim
- Nim Version 1.6 Released
What are some alternatives?
nimbus-eth1 - Nimbus: an Ethereum Execution Client for Resource-Restricted Devices
nlvm - LLVM-based compiler for the Nim language
nim-plotly - plotly wrapper for nim-lang
vscode-nim
moe - A command line based editor inspired by Vim. Written in Nim.
nim-chronos - Chronos - An efficient library for asynchronous programming
Unchained - A fully type safe, compile time only units library.
packages - List of packages for Nimble
adventofcode2022 - Advent of Code 2022 solutions in Nim
norm - A Nim ORM for SQLite and Postgres
Neel - A Nim library for making Electron-like HTML/JS GUI apps, with full access to Nim capabilities.
nimview - A Nim/Webview based helper to create Desktop/Server applications with Nim/C/C++ and HTML/CSS