MMseqs2
samtools
| MMseqs2 | samtools | |
|---|---|---|
| 4 | - | |
| 1,268 | 10 | |
| 2.6% | - | |
| 7.7 | 0.0 | |
| 7 days ago | almost 8 years ago | |
| C | C | |
| 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
samtools
We haven't tracked posts mentioning samtools yet.
Tracking mentions began in Dec 2020.
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).
Genbank - Genbank format tools and parser
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
ViennaRNAParser
hh-suite - Remote protein homology detection suite.
seqtk - Toolkit for processing sequences in FASTA/Q formats
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
libdna - ♥ Essential Functions for DNA Manipulation
SqueezeMeta - A complete pipeline for metagenomic analysis
RNAlien - RNAlien - unsupervised RNA family model construction
phybin - Binning (Newick) Phylogenetic Trees by Topology