dada2
Accurate sample inference from amplicon data with single nucleotide resolution (by benjjneb)
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)
| dada2 | kraken-biom | |
|---|---|---|
| 1 | 1 | |
| 453 | 43 | |
| - | - | |
| 4.3 | 0.0 | |
| 4 months ago | about 2 years ago | |
| R | Python | |
| GNU Lesser 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.
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.
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).
What are some alternatives?
When comparing dada2 and kraken-biom you can also consider the following projects:
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
TCGAbiolinks - TCGAbiolinks
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
atlas - ATLAS - Three commands to start analyzing your metagenome data
MicrobiomeStat - Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
drep - Rapid comparison and dereplication of genomes
GraphBin2 - ☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
taxopedia - Taxonomic trees (cladograms) from Wikipedia-scraped data.