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The Top 23 Sequence Bioinformatics Open Source Projects

Open source projects categorized as Sequence Bioinformatics
Categories > Data Processing > Bioinformatics
Categories > Data Processing > Sequence
Oneliners ⭐ 1,705
Useful bash one-liners for bioinformatics.
most recent commit 9 months ago
Bwa ⭐ 1,282
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
total releases 1most recent commit a year ago
Seqtk ⭐ 1,148
Toolkit for processing sequences in FASTA/Q formats
total releases 1most recent commit a year ago
Seqkit ⭐ 1,133
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
total releases 122most recent commit 3 months ago
Bowtie2 ⭐ 594
A fast and sensitive gapped read aligner
most recent commit 3 months ago
Biotite ⭐ 515
A comprehensive library for computational molecular biology
dependent packages 21total releases 52most recent commit 3 months agopypi biotite} Downloads
Dnafeaturesviewer ⭐ 500
👁️ Python library to plot DNA sequence features (e.g. from Genbank files)
dependent packages 22total releases 30most recent commit 6 months agopypi dna-features-viewer} Downloads
Nanopolish ⭐ 496
Signal-level algorithms for MinION data
most recent commit 9 months ago
Dash Bio ⭐ 485
Open-source bioinformatics components for Dash
dependent packages 11total releases 72most recent commit 8 months agopypi dash-bio} Downloads
Cutadapt ⭐ 475
Cutadapt removes adapter sequences from sequencing reads
dependent packages 24total releases 64most recent commit 3 months agopypi cutadapt} Downloads
Hh Suite ⭐ 429
Remote protein homology detection suite.
most recent commit a year ago
Pyfaidx ⭐ 427
Efficient pythonic random access to fasta subsequences
dependent packages 119total releases 86most recent commit 3 months agopypi pyfaidx} Downloads
Edlib ⭐ 421
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
dependent packages 35total releases 20most recent commit a year agopypi edlib} Downloads
Seqan3 ⭐ 373
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
most recent commit 3 months ago
Minigraph ⭐ 367
Proof-of-concept seq-to-graph mapper and graph generator
total releases 1most recent commit 4 months ago
Bakta ⭐ 365
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
total releases 37most recent commit 3 months ago
Bioconvert ⭐ 344
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
total releases 34most recent commit 5 months ago
Mixcr ⭐ 291
MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
most recent commit 3 months ago
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 4 years ago
Kaiju ⭐ 236
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
most recent commit 5 months ago
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104most recent commit 3 months agopypi hgvs} Downloads
Serratus ⭐ 219
Ultra-deep search for novel viruses
most recent commit a year ago
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68most recent commit 5 months agopypi pyfastx} Downloads
The 10 Most Depended On Sequence Bioinformatics Open Source Projects
Pyfaidx ⭐ 427
Efficient pythonic random access to fasta subsequences
dependent packages 119total releases 86latest release September 22, 2023most recent commit 3 months agopypi pyfaidx} Downloads
Edlib ⭐ 421
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
dependent packages 35total releases 20latest release August 20, 2021most recent commit a year agopypi edlib} Downloads
Cutadapt ⭐ 475
Cutadapt removes adapter sequences from sequencing reads
dependent packages 24total releases 64latest release December 06, 2023most recent commit 3 months agopypi cutadapt} Downloads
Dnafeaturesviewer ⭐ 500
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
dependent packages 22total releases 30latest release November 01, 2023most recent commit 6 months agopypi dna-features-viewer} Downloads
Biotite ⭐ 515
A comprehensive library for computational molecular biology
dependent packages 21total releases 52latest release September 09, 2023most recent commit 3 months agopypi biotite} Downloads
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Tskit ⭐ 131
Population-scale genomics
dependent packages 17total releases 36latest release October 10, 2023most recent commit 3 months agopypi tskit} Downloads
Pyhmmer ⭐ 98
Cython bindings and Python interface to HMMER3.
dependent packages 15total releases 51latest release October 29, 2023most recent commit 3 months agopypi pyhmmer} Downloads
Pyrodigal ⭐ 111
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
dependent packages 14total releases 60latest release November 27, 2023most recent commit 3 months agopypi pyrodigal} Downloads
Bio ⭐ 86
A lightweight and high-performance bioinformatics package in Golang
dependent packages 13total releases 32latest release November 11, 2023most recent commit 4 months ago
The 10 Latest Releases In Sequence Bioinformatics Open Source Projects
Cutadapt ⭐ 475
Cutadapt removes adapter sequences from sequencing reads
dependent packages 24total releases 64latest release December 06, 2023most recent commit 3 months agopypi cutadapt} Downloads
Algebra ⭐ 10
A Boolean Algebra for Genetic Variants
dependent packages 2total releases 18latest release December 04, 2023most recent commit 3 months agopypi mutalyzer-algebra} Downloads
Bakta ⭐ 365
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
total releases 37latest release November 29, 2023most recent commit 3 months ago
Pyrodigal ⭐ 111
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
dependent packages 14total releases 60latest release November 27, 2023most recent commit 3 months agopypi pyrodigal} Downloads
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Ska.rust ⭐ 35
Split k-mer analysis – version 2
total releases 14latest release November 23, 2023most recent commit 5 months ago
Seqkit ⭐ 1,133
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
total releases 122latest release November 18, 2023most recent commit 3 months ago
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Bio ⭐ 86
A lightweight and high-performance bioinformatics package in Golang
dependent packages 13total releases 32latest release November 11, 2023most recent commit 4 months ago
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