kraken-biom
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken). (by smdabdoub)
Metabuli
Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid. (by steineggerlab)
| kraken-biom | Metabuli | |
|---|---|---|
| 1 | 1 | |
| 50 | 127 | |
| - | 7.1% | |
| 0.0 | 9.2 | |
| almost 3 years ago | 9 days ago | |
| Python | C++ | |
| MIT License | GNU 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.
kraken-biom
Posts with mentions or reviews of kraken-biom.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Differences between read based abundancy estimation programs? (metagenomics)
The issue is that after performing a taxonomic classification using kraken2, I want to create abundance tables regarding this taxonomic classification outputs. Some people have recommended me to use kraken--biom (https://github.com/smdabdoub/kraken-biom) and some others recommended me to use bracken (https://ccb.jhu.edu/software/bracken/index.shtml?t=manual).
Metabuli
Posts with mentions or reviews of Metabuli.
We have used some of these posts to build our list of alternatives
and similar projects.
What are some alternatives?
When comparing kraken-biom and Metabuli you can also consider the following projects:
atlas - ATLAS - Three commands to start analyzing your metagenome data
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
sshash - A compressed, associative, exact, and weighted dictionary for k-mers.
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
megahit - Ultra-fast and memory-efficient (meta-)genome assembler
drep - Rapid comparison and dereplication of genomes
fastp - An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
taxopedia - Taxonomic trees (cladograms) from Wikipedia-scraped data.