Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid. (by steineggerlab)
sshash
A compressed, associative, exact, and weighted dictionary for k-mers. (by jermp)
Metabuli | sshash | |
---|---|---|
1 | 1 | |
89 | 80 | |
- | - | |
8.8 | 6.9 | |
21 days ago | 17 days ago | |
C++ | C++ | |
GNU General Public License v3.0 only | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
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.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
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.
Metabuli
Posts with mentions or reviews of Metabuli.
We have used some of these posts to build our list of alternatives
and similar projects.
sshash
Posts with mentions or reviews of sshash.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-09-08.
-
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!
What are some alternatives?
When comparing Metabuli and sshash you can also consider the following projects:
eternal - A C++14 compile-time/constexpr map and hash map with minimal binary footprint
pthash - Fast and compact minimal perfect hash functions in C++.
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.
DAR - DAR - Disk ARchive