sshash
pthash
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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!
pthash
- Fast and compact minimal perfect hash functions in C++
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announcing ph - open-source, rust library for perfect hashing
The best in terms of evaluation time is PTHash (I think it can achieve 1 cache miss/lookup). Unfortunately the only implementation I know of for this method is in C++ (there is certainly no implementation in Rust): https://github.com/jermp/pthash
What are some alternatives?
eternal - A C++14 compile-time/constexpr map and hash map with minimal binary footprint
prvhash - PRVHASH - Pseudo-Random-Value Hash. Hash functions, PRNG with unlimited period, randomness extractor, and a glimpse into abyss. (inline C/C++) (Codename Gradilac/Градилак)
rspec - (Rust) Rspec - a BDD test harness for stable Rust
Data_Structures_in_Cpp - Contains some useful custom Data-Structures/Containers & Algorithms, developed during my 3rd semester at University.
komihash - Very fast, high-quality hash function, discrete-incremental and streamed hashing-capable (non-cryptographic, inline C/C++) 26GB/s + PRNG
DAR - DAR - Disk ARchive
lazy_importer - library for importing functions from dlls in a hidden, reverse engineer unfriendly way