samtools
MMseqs2
Our great sponsors
| samtools | MMseqs2 | |
|---|---|---|
| 3 | 4 | |
| 1,549 | 1,251 | |
| 2.5% | 3.8% | |
| 8.6 | 7.7 | |
| 3 days ago | 25 days ago | |
| C | C | |
| GNU General Public License v3.0 or later | 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.
samtools
-
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)
-
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.
-
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
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
What are some alternatives?
seqtk - Toolkit for processing sequences in FASTA/Q formats
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
RNAlien - RNAlien - unsupervised RNA family model construction
hh-suite - Remote protein homology detection suite.
libBigWig - A C library for handling bigWig files
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
htslib - C library for high-throughput sequencing data formats
bioinformatics-toolkit - A collection of bioinformatics algorithms