MMseqs2
SqueezeMeta

MMseqs2 | SqueezeMeta | |
---|---|---|
5 | 1 | |
1,527 | 392 | |
1.6% | 1.3% | |
9.2 | 4.0 | |
19 days ago | 14 days ago | |
C | C | |
MIT License | GNU General Public License v3.0 only |
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MMseqs2
- Segmenting Credit Card Customers with K-Means: A Fun Dive into Clustering
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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
SqueezeMeta
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Conda/miniconda output and error files creation
Give it a look https://github.com/jtamames/SqueezeMeta
What are some alternatives?
htslib - C library for high-throughput sequencing data formats
ttyplot - a realtime plotting utility for terminal/console with data input from stdin
samtools - Tools (written in C using htslib) for manipulating next-generation sequencing data
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline
seqtk - Toolkit for processing sequences in FASTA/Q formats
mag - Assembly and binning of metagenomes
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
drep - Rapid comparison and dereplication of genomes
dada2 - Accurate sample inference from amplicon data with single nucleotide resolution
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
hh-suite - Remote protein homology detection suite.
MethylDackel - A (mostly) universal methylation extractor for BS-seq experiments.
