MMseqs2
SqueezeMeta
| MMseqs2 | SqueezeMeta | |
|---|---|---|
| 4 | 1 | |
| 1,265 | 341 | |
| 2.4% | - | |
| 7.7 | 6.6 | |
| 13 days ago | 5 days ago | |
| C | C | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 only |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
MMseqs2
-
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
-
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
SqueezeMeta
-
Conda/miniconda output and error files creation
Give it a look https://github.com/jtamames/SqueezeMeta
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).
mag - Assembly and binning of metagenomes
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
ttyplot - a realtime plotting utility for terminal/console with data input from stdin
hh-suite - Remote protein homology detection suite.
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
drep - Rapid comparison and dereplication of genomes
seqtk - Toolkit for processing sequences in FASTA/Q formats
htslib - C library for high-throughput sequencing data formats
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
samtools - [Moved to: https://github.com/ingolia/SamTools]