dada2
rBLAST


dada2 | rBLAST | |
---|---|---|
1 | 1 | |
484 | 106 | |
1.0% | 0.9% | |
6.7 | 5.8 | |
10 days ago | about 1 month ago | |
R | R | |
GNU Lesser General Public License v3.0 only | GNU General Public License v3.0 only |
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dada2
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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.
rBLAST
What are some alternatives?
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
rhmmer - Simple R utilities for working with HMMER
TCGAbiolinks - TCGAbiolinks
bambu - Reference-guided transcript discovery and quantification for long read RNA-Seq data
MicrobiomeStat - Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
seqinr - Biological sequences retrieval and analysis
Metabuli - Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
flextaxd - FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )
bracken_plot - A Shiny app for taxonomic abundance visualization

