sourmash v4 — Peer-reviewed • Rank 21.8 • Science 100%

sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets - Published in JOSS (2024)

anndata — Peer-reviewed • Rank 24.6 • Science 95%

anndata: Access and store annotated data matrices - Published in JOSS (2024)

khmer release v2.1 — Peer-reviewed • Rank 18.9 • Science 100%

khmer release v2.1: software for biological sequence analysis - Published in JOSS (2017)

Pyrodigal — Peer-reviewed • Rank 15.6 • Science 100%

Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes - Published in JOSS (2022)

chembl-downloader • Rank 13.9 • Science 98%

Write reproducible code for getting and processing ChEMBL

Rasusa — Peer-reviewed • Rank 17.1 • Science 93%

Rasusa: Randomly subsample sequencing reads to a specified coverage - Published in JOSS (2022)

VCFPy — Peer-reviewed • Rank 15.9 • Science 93%

VCFPy: a Python 3 library with good support for both reading and writing VCF - Published in JOSS (2016)

The UCSCXenaTools R package — Peer-reviewed • Rank 13.8 • Science 95%

The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq - Published in JOSS (2019)

ReferenceSeeker — Peer-reviewed • Rank 8.7 • Science 100%

ReferenceSeeker: rapid determination of appropriate reference genomes - Published in JOSS (2020)

Fasten — Peer-reviewed • Rank 15.4 • Science 93%

Fasten: a toolkit for streaming operations on fastq files - Published in JOSS (2024)

TipToft — Peer-reviewed • Rank 8.3 • Science 100%

TipToft: detecting plasmids contained in uncorrected long read sequencing data - Published in JOSS (2019)

Multiblock PLS — Peer-reviewed • Rank 10.3 • Science 98%

Multiblock PLS: Block dependent prediction modeling for Python - Published in JOSS (2019)

Fastsubtrees — Peer-reviewed • Rank 8.2 • Science 100%

Fastsubtrees: simple and efficient subtrees extractions in Python with applications to NCBI taxonomy - Published in JOSS (2022)

TAXPASTA — Peer-reviewed • Rank 9.5 • Science 98%

TAXPASTA: TAXonomic Profile Aggregation and STAndardisation - Published in JOSS (2023)

slurmR — Peer-reviewed • Rank 11.4 • Science 96%

slurmR: A lightweight wrapper for HPC with Slurm - Published in JOSS (2021)

Pycashier — Peer-reviewed • Rank 7.2 • Science 100%

Pycashier: cash in on DNA barcode tags - Published in JOSS (2024)

Bacting — Peer-reviewed • Rank 8.5 • Science 98%

Bacting: a next generation, command line version of Bioclipse - Published in JOSS (2021)

Contextualized — Peer-reviewed • Rank 11.4 • Science 95%

Contextualized: Heterogeneous Modeling Toolbox - Published in JOSS (2024)

Multilocus sequence typing by blast from de novo assemblies against PubMLST — Peer-reviewed • Rank 6.1 • Science 100%

Multilocus sequence typing by blast from de novo assemblies against PubMLST - Published in JOSS (2016)

AltamISA — Peer-reviewed • Rank 12.6 • Science 93%

AltamISA: a Python API for ISA-Tab files - Published in JOSS (2019)

MicrobiomeR — Peer-reviewed • Rank 5.3 • Science 100%

MicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflows - Published in JOSS (2019)

Bedparse — Peer-reviewed • Rank 9.9 • Science 95%

Bedparse: feature extraction from BED files - Published in JOSS (2019)

Powering single-cell analyses in the browser with WebAssembly — Peer-reviewed • Rank 6.6 • Science 98%

Powering single-cell analyses in the browser with WebAssembly - Published in JOSS (2023)

Pynteny — Peer-reviewed • Rank 6.4 • Science 98%

Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases - Published in JOSS (2023)

cstag and cstag-cli — Peer-reviewed • Rank 11.2 • Science 93%

cstag and cstag-cli: tools for manipulating and visualizing cs tags - Published in JOSS (2024)

Metagenomic classification with KrakenUniq on low-memory computers — Peer-reviewed • Rank 8.7 • Science 95%

Metagenomic classification with KrakenUniq on low-memory computers - Published in JOSS (2022)

Python Implementation of Codon Adaptation Index — Peer-reviewed • Rank 10.3 • Science 93%

Python Implementation of Codon Adaptation Index - Published in JOSS (2018)

SaffronTree — Peer-reviewed • Rank 5.1 • Science 98%

SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs. - Published in JOSS (2017)

Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer — Peer-reviewed • Rank 8.9 • Science 93%

Lexicon-Mono-Seq, DOM Text Based Async MSA Viewer - Published in JOSS (2019)

multiqc • Rank 24.6 • Science 77%

Aggregate results from bioinformatics analyses across many samples into a single report.

Rainbow — Peer-reviewed • Rank 5.5 • Science 95%

Rainbow: Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flow - Published in JOSS (2022)

org.biojava • Rank 22.4 • Science 77%

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

Recan — Peer-reviewed • Rank 6.1 • Science 93%

Recan: Python tool for analysis of recombination events in viral genomes - Published in JOSS (2020)

Taxonomy Resolver — Peer-reviewed • Rank 2.5 • Science 96%

Taxonomy Resolver: A Python package for building and filtering taxonomy trees - Published in JOSS (2025)

WGS2NCBI - Toolkit for preparing genomes for submission to NCBI — Peer-reviewed • Rank 5.0 • Science 93%

WGS2NCBI - Toolkit for preparing genomes for submission to NCBI - Published in JOSS (2019)

Genotify — Peer-reviewed • Rank 4.9 • Science 93%

Genotify: Fast, lightweight gene lookup and summarization - Published in JOSS (2018)

covtobed — Peer-reviewed • Rank 4.5 • Science 93%

covtobed: a simple and fast tool to extract coverage tracks from BAM files - Published in JOSS (2020)

sbgnviz • Rank 12.2 • Science 85%

A web based visualization tool for process description maps in SBGN

Phylen — Peer-reviewed • Rank 2.2 • Science 95%

Phylen: automatic phylogenetic reconstruction using the EggNOG database - Published in JOSS (2018)

biotmle — Peer-reviewed • Rank 4.0 • Science 93%

biotmle: Targeted Learning for Biomarker Discovery - Published in JOSS (2017)

ORIS — Peer-reviewed • Rank 1.1 • Science 95%

ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes - Published in JOSS (2019)

chatAI4R: Interactive Artificial Intelligence toolkit for Data Science in R • Rank 8.4 • Science 87%

chatAI4R: Interactive Artificial Intelligence toolkit for Data Science in R - Published in JOSS (2026)

HARE — Peer-reviewed • Rank 2.2 • Science 93%

HARE: A Python workflow for analyzing genomic feature enrichment in GWAS datasets - Published in JOSS (2024)

chise • Rank 10.0 • Science 85%

A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

cooler • Rank 17.7 • Science 77%

A cool place to store your Hi-C

io.nextflow:nextflow • Rank 17.5 • Science 77%

A DSL for data-driven computational pipelines

pysradb • Rank 17.5 • Science 77%

Package for fetching metadata and downloading data from SRA/ENA/GEO

bioframe • Rank 17.3 • Science 77%

Genomic interval operations on Pandas DataFrames

pypop-genomics • Rank 15.2 • Science 77%

PyPop: Python for Population Genomics

bakta • Rank 15.1 • Science 77%

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

qmflows • Rank 14.8 • Science 77%

This library tackles the construction and efficient execution of computational chemistry workflows

integron_finder • Rank 6.8 • Science 85%

Bioinformatics tool to find integrons in bacterial genomes

rna-tools • Rank 14.2 • Science 77%

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

atropos • Rank 13.1 • Science 77%

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

snakefmt • Rank 22.5 • Science 67%

The uncompromising Snakemake code formatter

aviary-genome • Rank 12.4 • Science 77%

A hybrid assembly and MAG recovery pipeline (and more!)

pyhmmer • Rank 22.3 • Science 67%

Cython bindings and Python interface to HMMER3.

nf-core • Rank 22.0 • Science 67%

Python package with helper tools for the nf-core community.

cutadapt • Rank 22.0 • Science 67%

Cutadapt removes adapter sequences from sequencing reads

NGLess • Rank 13.9 • Science 75%

NGLess: NGS with less work

pathway-mapper • Rank 13.6 • Science 75%

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

qubekit • Rank 10.8 • Science 77%

Quantum Mechanical Bespoke Force Field Derivation Toolkit

pyskani • Rank 10.7 • Science 77%

PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.

graphein • Rank 10.4 • Science 77%

Protein Graph Library

dockstore • Rank 10.3 • Science 77%

An app store for scientific workflows, tools, notebooks, and services

pyfastani • Rank 10.3 • Science 77%

Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.

cazy-webscraper • Rank 9.9 • Science 77%

Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.

abyss • Rank 9.7 • Science 77%

:microscope: Assemble large genomes using short reads

gnparser • Rank 8.8 • Science 77%

GNparser normalises scientific names and extracts their semantic elements.

dash • Rank 31.2 • Science 54%

Data Apps & Dashboards for Python. No JavaScript Required.

dnaio • Rank 18.1 • Science 67%

Efficiently read and write sequencing data from Python

biocommons.seqrepo • Rank 18.1 • Science 67%

non-redundant, compressed, journalled, file-based storage for biological sequences

adapt-diagnostics • Rank 9.5 • Science 75%

A package for designing activity-informed nucleic acid diagnostics for viruses.

https://github.com/theislab/cellrank • Rank 16.8 • Science 67%

CellRank: dynamics from multi-view single-cell data

jcvi • Rank 16.7 • Science 67%

Python library to facilitate genome assembly, annotation, and comparative genomics

vembrane • Rank 6.6 • Science 77%

vembrane filters VCF records using python expressions

asap • Rank 6.4 • Science 77%

A scalable bacterial genome assembly, annotation and analysis pipeline

flo • Rank 6.3 • Science 77%

Same species annotation lift over pipeline.

chip-atlas • Rank 6.2 • Science 77%

ChIP-Atlas: Browse and analyze all public ChIP/DNase-seq data on your browser

sumt • Rank 6.1 • Science 77%

Computes consensus trees and other phylogenetic tree summaries

newt • Rank 7.8 • Science 75%

A web application to visualize and edit pathway models

segul • Rank 15.8 • Science 67%

An ultrafast and memory efficient tool for phylogenomics

dbdipy • Rank 5.6 • Science 77%

A Python library for the inspection, curation and interpretation of DBDI-MS data.

yacrd • Rank 15.6 • Science 67%

Yet Another Chimeric Read Detector

brendapyrser • Rank 4.9 • Science 77%

A Python parser for the BRENDA database

sigprofilermatrixgenerator • Rank 14.9 • Science 67%

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

clinker • Rank 14.8 • Science 67%

Gene cluster comparison figure generator

cdk • Rank 27.4 • Science 54%

The Chemistry Development Kit

biopython • Rank 32.2 • Science 49%

Official git repository for Biopython (originally converted from CVS)

maftools • Rank 22.2 • Science 59%

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

MSnbase • Rank 21.7 • Science 59%

Base Classes and Functions for Mass Spectrometry and Proteomics

cool-seq-tool • Rank 13.6 • Science 67%

cobra • Rank 21.0 • Science 59%

COBRApy is a package for constraint-based modeling of metabolic networks.

minimap2 • Rank 20.9 • Science 59%

A versatile pairwise aligner for genomic and spliced nucleotide sequences

glycowork • Rank 12.7 • Science 67%

Package for processing and analyzing glycans and their role in biology.

pybbi • Rank 12.7 • Science 67%

Python bindings to UCSC BigWig and BigBed library

vsearch • Rank 12.5 • Science 67%

Versatile open-source tool for microbiome analysis

gtfsort • Rank 12.3 • Science 67%

a lexicographically-based GTF/GFF sorter

dbcanlight • Rank 2.2 • Science 77%

A lightweight rewrite of run_dbcan for better multithread performance

efp-seq_browser • Rank 4.2 • Science 75%

An RNA-Seq data exploration tool that shows read map coverage of a gene of interest along with a coloured "electronic fluorescent pictographic" (eFP) based on its RPKM expression level.