Top 15 sequence-alignment Open-Source Projects

• Biopython

  31 4,185 9.6 Python

  Official git repository for Biopython (originally converted from CVS)

  

Project mention: Invitación a proyecto - Biopython en Español | /r/devsarg | 2023-07-23

• minimap2

  5 1,691 7.6 C

  A versatile pairwise aligner for genomic and spliced nucleotide sequences

Project mention: Ask HN: Comment here about whatever you're passionate about at the moment | news.ycombinator.com | 2023-11-06

Interested as well! But the future is not so dark, things like e.g. https://github.com/lh3/minimap2 are a breath of fresh air.

• InfluxDB

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• bwa

  3 1,454 2.7 C

  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Project mention: my friend showed me his code, thees are all functions | /r/ProgrammerHumor | 2023-05-25

Check out these sweet macros (from the same repo): https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/kbtree.h

• diamond

  3 962 6.3 C++

  Accelerated BLAST compatible local sequence aligner. (by bbuchfink)

Project mention: comparing the similarity between a set of protein sequences | /r/genomics | 2023-05-12

Diamond (https://github.com/bbuchfink/diamond) might help. It has a protein sequence clustering option. You could cluster your sequences and then take the centroids of each cluster. Vary the BLAST parameters to increase/decrease the numbers of clusters.

• bwa-mem2

  2 680 3.3 C++

  The next version of bwa-mem

  

• BioJava

  2 578 8.2 Java

  :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

  

Project mention: Outperforming Rust DNA sequence parsing benchmarks by 50% with Mojo | news.ycombinator.com | 2024-02-08

Here is a cache of valid and invalid FASTQ files for unit tests

https://github.com/biojava/biojava/tree/master/biojava-genom...

• edlib

  2 484 1.1 C++

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

• SaaSHub

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• seqan3

  1 389 8.9 C++

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

  

• bistring

  1 367 4.7 Python

  Bidirectionally transformed strings

  

• miniprot

  1 302 5.8 C

  Align proteins to genomes with splicing and frameshift

• deepblast

  2 99 4.8 Python

  Neural Networks for Protein Sequence Alignment

  

Project mention: [D] To all the machine learning engineers: most difficult model task/type you’ve ever had to work with? | /r/MachineLearning | 2023-07-03

• orthologr

  1 83 7.3 R

  Genome wide orthology inference and dNdS estimation

  

• sequence_align

  1 57 4.6 Python

  Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

  

• spacepile

  1 13 4.9 Rust

  convert reads from repeated measures of same piece of DNA into spaced matricies for deep learners.

Project mention: dna_parser : A Python package written in Rust to encode DNA sequences for machine learning. | /r/rust | 2023-05-17

I know very little about machine learning encoding but saw a somewhat similar project here https://github.com/brentp/spacepile

• redotable

  1 10 10.0 Java

  A dotplot application for DNA/RNA sequence

• SaaSHub

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sequence-alignment related posts

• [D] To all the machine learning engineers: most difficult model task/type you’ve ever had to work with?

  2 projects | /r/MachineLearning | 3 Jul 2023

• my friend showed me his code, thees are all functions

  3 projects | /r/ProgrammerHumor | 25 May 2023

• comparing the similarity between a set of protein sequences

  2 projects | /r/genomics | 12 May 2023

• BLAST 10,000 genes?

  1 project | /r/bioinformatics | 25 Feb 2023

• Truncating genome fastas to just overlapping regions

  1 project | /r/bioinformatics | 19 Jan 2023

• which database is best to use on BLAST to identify an unknown protein?

  1 project | /r/bioinformatics | 6 Nov 2022

• Alignment of long reads to plasmid and generation of consensus sequence.

  1 project | /r/bioinformatics | 26 Oct 2022
• A note from our sponsor - SaaSHub
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