sshash
eternal
| sshash | eternal | |
|---|---|---|
| 1 | 1 | |
| 78 | 189 | |
| - | 0.0% | |
| 7.1 | 10.0 | |
| 17 days ago | over 1 year ago | |
| C++ | C++ | |
| MIT License | ISC License |
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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.
sshash
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Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2
The paper describing a new tool from our lab has just been published in Genome Biology (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02743-6). Cuttlefish 2 is a tool for efficiently computing the compacted de Bruijn graph (or a spectrum preserving string set) from either raw sequencing reads or from reference genomes. It is quite fast and very memory efficient — for example, we were able to construct the compacted de Bruijn graph on a set of 661K bacterial genomes in 16 hours and 30 minutes using only 48.7GB of RAM. Construction of the compacted de Bruijn graph is an important initial processing step in e.g. genome assembly, and is also important in several other areas such as comparative genomics and as a critical step in building certain types of indices (e.g. [sshash](https://github.com/jermp/sshash)). You can find the cuttlefish 2 software on GitHub [here](https://github.com/COMBINE-lab/cuttlefish), and it can also be installed via Bioconda. We'd be happy to have your feedback!
eternal
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Long switch statements. Is there a better way?
Unfortunately std::map is not constexpr. There are open source alternatives though (not affiliated with the author in any way).
What are some alternatives?
pthash - Fast and compact minimal perfect hash functions in C++.
hof - Higher-order functions for c++
rspec - (Rust) Rspec - a BDD test harness for stable Rust
StaticTypeInfo - 🏀 Up your type-game. A small C++ library for compile-time type names and type indices.
Data_Structures_in_Cpp - Contains some useful custom Data-Structures/Containers & Algorithms, developed during my 3rd semester at University.
bitset2 - std::bitset with constexpr implementations plus additional features.
DAR - DAR - Disk ARchive
uninttp - A universal type for non-type template parameters for C++20 or later.
vswitch - Function-like value switch.
compile-time-regular-expressions - Compile Time Regular Expression in C++
constexpr-8cc - Compile-time C Compiler implemented as C++14 constant expressions