MMseqs2
samtools
| MMseqs2 | samtools | |
|---|---|---|
| 4 | 3 | |
| 1,268 | 1,558 | |
| 2.6% | 1.5% | |
| 7.7 | 8.6 | |
| 7 days ago | 4 days ago | |
| C | C | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
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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
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BWA MEM with merged paired-end reads and unmerged in the same run.
I don’t know about your first question, but for your second, use “bwa mem -p …” for smart pairing of an interleaved FASTQ/A with both paired end reads and singletons. BWA will recognize whether adjacent reads are paired if they have the same prefix (see here)
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Show a Tanuki with Samtools!
In this post, I'm going to add the command tanuki to Samtools to display a ASCII art(AA) tanuki.
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How do I know if I'm gonna get my module?
Quite a number of bioinformatics related tool that were written in C/C++, eg. (https://github.com/samtools/samtools). But there are also a lot of modern packages for Python / R now
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).
seqtk - Toolkit for processing sequences in FASTA/Q formats
hh-suite - Remote protein homology detection suite.
RNAlien - RNAlien - unsupervised RNA family model construction
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
libBigWig - A C library for handling bigWig files
SqueezeMeta - A complete pipeline for metagenomic analysis
libdna - ♥ Essential Functions for DNA Manipulation
htslib - C library for high-throughput sequencing data formats
bioinformatics-toolkit - A collection of bioinformatics algorithms