MMseqs2
kraken-biom
| MMseqs2 | kraken-biom | |
|---|---|---|
| 4 | 1 | |
| 1,265 | 43 | |
| 2.4% | - | |
| 7.7 | 0.0 | |
| 13 days ago | about 2 years ago | |
| C | Python | |
| GNU General Public License v3.0 only | MIT License |
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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
kraken-biom
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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?
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.
atlas - ATLAS - Three commands to start analyzing your metagenome data
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
SqueezeMeta - A complete pipeline for metagenomic analysis
drep - Rapid comparison and dereplication of genomes
seqtk - Toolkit for processing sequences in FASTA/Q formats
GraphBin2 - ☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
htslib - C library for high-throughput sequencing data formats
taxopedia - Taxonomic trees (cladograms) from Wikipedia-scraped data.