MMseqs2
dada2
| MMseqs2 | dada2 | |
|---|---|---|
| 4 | 1 | |
| 1,268 | 454 | |
| 2.6% | - | |
| 7.7 | 4.3 | |
| 7 days ago | 4 months ago | |
| C | R | |
| GNU General Public License v3.0 only | GNU Lesser General Public License v3.0 only |
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MMseqs2
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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
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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.
What are some alternatives?
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
hh-suite - Remote protein homology detection suite.
TCGAbiolinks - TCGAbiolinks
rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
SqueezeMeta - A complete pipeline for metagenomic analysis
MicrobiomeStat - Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
seqtk - Toolkit for processing sequences in FASTA/Q formats
htslib - C library for high-throughput sequencing data formats