MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite (by soedinglab)
dada2
Accurate sample inference from amplicon data with single nucleotide resolution (by benjjneb)
| MMseqs2 | dada2 | |
|---|---|---|
| 6 | 1 | |
| 1,587 | 488 | |
| 4.1% | 0.2% | |
| 9.2 | 6.7 | |
| 4 days ago | about 2 months ago | |
| C | R | |
| MIT License | GNU Lesser General Public License v3.0 only |
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.
MMseqs2
Posts with mentions or reviews of MMseqs2.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2025-03-02.
-
13 Github Projects that Will Supercharge Your Development Journey in 2025 🚀
# Clone the MMseqs2 repository git clone https://github.com/soedinglab/MMseqs2.git # Change to the MMseqs2 directory cd MMseqs2 # Set up a build directory and compile the software mkdir build && cd build cmake .. make # Optionally, install the software system-wide sudo make install
- Segmenting Credit Card Customers with K-Means: A Fun Dive into Clustering
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Clustering tool that could help cluster protein sequences based on percentage identity
A tool I often recommend for sequence clustering is mmseqs2 : https://github.com/soedinglab/MMseqs2, fast and efficient :)
- MMseqs2 – an example of great software for biology
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Metagenomics: abundances of short reads using genome databases
Tools like the the mmseqs2 "taxonomy" module, or DIAMOND v2, can efficiently align contigs to genome databases to assign taxonomy, but it seems like they aren't intended to provide abundance estimates for each taxon (since that would require mapping reads, and mmseqs2 can't even use paired-reads). Can anyone recommend tools or methods for A) connecting per-contig coverage information to contig taxonomy, or B) mapping short reads against genome databases?
- Retrieving One-to-One Orthologs of Unprocessed cDNAs
dada2
Posts with mentions or reviews of dada2.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Error model generation and subsequent steps in DADA2 pipeline for multiple sequencing runs
It is recommended to process each run separately (https://github.com/benjjneb/dada2/issues/1177). Each flow cell behaves differently, so the error model for one might not work well for another run. You can merge them together once you have your sequence table.
What are some alternatives?
When comparing MMseqs2 and dada2 you can also consider the following projects:
htslib - C library for high-throughput sequencing data formats
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
TCGAbiolinks - TCGAbiolinks