Top 4 C++ sequence-alignment Projects

diamond

2 769 4.0 C++

Accelerated BLAST compatible local sequence aligner. (by bbuchfink)

Project mention: which database is best to use on BLAST to identify an unknown protein? | reddit.com/r/bioinformatics | 2022-11-06

What I usually do is the DIAMOND search (https://github.com/bbuchfink/diamond) on UniRef (50/90) database.
bwa-mem2

2 588 0.0 C++

The next version of bwa-mem

Project mention: Anyone use DRAGEN-GATK? | reddit.com/r/bioinformatics | 2022-10-12

If you haven’t heard of it already you may want to check out https://github.com/bwa-mem2/bwa-mem2 which is a faster version of bwa-mem. I’ve been using it for a while now and found it to be quite stable, same results as the original and the speed improvement is nice.
Sonar

www.sonarsource.com
sponsored

Write Clean C++ Code. Always.. Sonar helps you commit clean C++ code every time. With over 550 unique rules to find C++ bugs, code smells & vulnerabilities, Sonar finds the issues while you focus on the work.
edlib

1 406 3.0 C++

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

Project mention: What's an efficient way to find multiple subsequences in several FASTQs? | reddit.com/r/bioinformatics | 2022-02-08

I’ve got a similar situation. I was implementing the Smith-Waterman algorithm when I figured someone had to have already written a “fast” version of this. I found the edlib package (https://github.com/Martinsos/edlib) which does sequence alignment using Levenshtein distance. Essentially same DP algorithm as your traditional NW or SW only this is a C++ implementation with a Python wrapper. (I’m assuming you’re using Python, could be wrong though). The pertinent aspects of the output of this function contains the distance (dissimilarity) and the location (what index does the alignment start and end). This tool may go a ways to helping your pipeline. You could also look to metagenomic papers for inspiration as this is a problem (find a substring in a huge amount of data) that the community contends with all the time. Kmer based approach may also be useful if you want to attempt the alignment free path. Cheers.
seqan3

0 318 9.1 C++

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020). The latest post mention was on 2022-11-06.