dada2
seqinr
dada2 | seqinr | |
---|---|---|
1 | 1 | |
484 | 2 | |
1.0% | - | |
6.7 | 6.1 | |
30 days ago | 3 months ago | |
R | R | |
GNU Lesser General Public License v3.0 only | GPL-2 |
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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.
seqinr
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protr VS seqinr - a user suggested alternative
2 projects | 5 May 2024
What are some alternatives?
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
protr - 🧬 Toolkit for generating various numerical features of protein sequences
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
orthologr - Genome wide orthology inference and dNdS estimation
TCGAbiolinks - TCGAbiolinks
seqan3 - The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
MicrobiomeStat - Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Peptides - An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
BioJava - :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
Metabuli - Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.