graphsim — Peer-reviewed • Rank 14.3 • Science 98%

graphsim: An R package for simulating gene expression data from graph structures of biological pathways - Published in JOSS (2020)

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

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

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)

CheckQC — Peer-reviewed • Rank 13.0 • Science 93%

CheckQC: Quick quality control of Illumina sequencing runs - Published in JOSS (2018)

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)

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

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

GFAKluge — Peer-reviewed • Rank 6.9 • Science 95%

GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats - Published in JOSS (2019)

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.

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)

Baargin — Peer-reviewed • Rank 3.7 • Science 93%

Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance - Published in JOSS (2023)

higlass • Rank 18.2 • Science 77%

Fast, flexible and extensible genome browser.

cooler • Rank 17.7 • Science 77%

A cool place to store your Hi-C

bioframe • Rank 17.3 • Science 77%

Genomic interval operations on Pandas DataFrames

gosling.js • Rank 13.7 • Science 77%

Grammar of Scalable Linked Interactive Nucleotide Graphics

NGLess • Rank 13.9 • Science 75%

NGLess: NGS with less work

gget • Rank 20.2 • Science 67%

🧬 gget enables efficient querying of genomic reference databases

cazy-webscraper • Rank 9.9 • Science 77%

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

mudata • Rank 18.6 • Science 67%

Multimodal Data (.h5mu) implementation for 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.

jcvi • Rank 16.7 • Science 67%

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

OpenOmics — Peer-reviewed • Rank 6.7 • Science 77%

OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. - Published in JOSS (2021)

bactmap • Rank 6.2 • Science 77%

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

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.

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

minimap2 • Rank 20.9 • Science 59%

A versatile pairwise aligner for genomic and spliced nucleotide sequences

pybbi • Rank 12.7 • Science 67%

Python bindings to UCSC BigWig and BigBed library

gecco-tool • Rank 11.1 • Science 67%

GEne Cluster prediction with COnditional random fields.

sarek • Rank 10.9 • Science 67%

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

arvados • Rank 23.1 • Science 54%

An open source platform for managing and analyzing biomedical big data

GEOquery • Rank 23.0 • Science 54%

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

biomartr • Rank 17.9 • Science 59%

Genomic Data Retrieval with R

trviz • Rank 9.7 • Science 67%

A python library for decomposing and visualizing tandem repeat sequences

nplinker • Rank 11.4 • Science 64%

A python framework for microbial natural products data mining by integrating genomics and metabolomics data

https://github.com/althonos/lightmotif • Rank 16.3 • Science 59%

A lightweight platform-accelerated library for biological motif scanning using position weight matrices.

poppunk • Rank 7.5 • Science 67%

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

msprime • Rank 19.3 • Science 54%

Simulate genealogical trees and genomic sequence data using population genetic models

filtersam • Rank 6.3 • Science 67%

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

ncbi-genome-download • Rank 19.2 • Science 54%

Scripts to download genomes from the NCBI FTP servers

GFF3toEMBL — Peer-reviewed • Rank 5.8 • Science 67%

GFF3toEMBL: Preparing annotated assemblies for submission to EMBL - Published in JOSS (2016)

circdna • Rank 5.4 • Science 67%

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

pyfaidx • Rank 23.0 • Science 49%

Efficient pythonic random access to fasta subsequences

xpressplot • Rank 4.7 • Science 67%

A toolkit for navigating and analyzing gene expression datasets

readfish • Rank 12.4 • Science 59%

CLI tool for flexible and fast adaptive sampling on ONT sequencers

gemma.R • Rank 14.2 • Science 57%

An R wrapper for the Gemma RESTful API

coolpuppy • Rank 11.8 • Science 59%

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

https://github.com/althonos/pyopal • Rank 11.8 • Science 59%

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.

hail • Rank 24.2 • Science 46%

Cloud-native genomic dataframes and batch computing

zol • Rank 7.1 • Science 62%

zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)

pyranges • Rank 19.9 • Science 49%

Performant Pythonic GenomicRanges

genbankpy • Rank 1.8 • Science 67%

Tools to download, parse and filter GenBank files

smoove • Rank 14.7 • Science 54%

structural variant calling and genotyping with existing tools, but, smoothly.

ClustAssess • Rank 11.2 • Science 57%

Tools for assessing clustering robustness

circlator • Rank 13.5 • Science 54%

A tool to circularize genome assemblies

phables • Rank 10.4 • Science 57%

🫧🧬 From fragmented assemblies to high-quality bacteriophage genomes

bedops • Rank 11.9 • Science 54%

:microscope: BEDOPS: high-performance genomic feature operations

staramr • Rank 11.7 • Science 54%

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

goatools • Rank 19.7 • Science 46%

Python library to handle Gene Ontology (GO) terms

cnr-flow • Rank 1.6 • Science 64%

CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.

https://github.com/brentp/vcfanno • Rank 16.2 • Science 49%

annotate a VCF with other VCFs/BEDs/tabixed files

truvari • Rank 16.1 • Science 49%

Structural variant toolkit for VCFs

qqman • Rank 18.0 • Science 46%

An R package for creating Q-Q and manhattan plots from GWAS results

divbrowse • Rank 6.6 • Science 57%

A web application for interactive visualization and exploratory data analysis of variant call matrices

chewbbaca • Rank 14.4 • Science 49%

BSR-Based Allele Calling Algorithm

circrna • Rank 6.1 • Science 57%

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

jvarkit • Rank 9.0 • Science 54%

Java utilities for Bioinformatics

ezaai • Rank 5.9 • Science 57%

EzAAI - High Throughput Prokaryotic AAI Calculator

AlphaSimR • Rank 13.7 • Science 49%

R package for breeding program simulations

kgp • Rank 8.6 • Science 54%

1000 Genomes Project Metadata R Package

galaxy • Rank 26.5 • Science 36%

Data intensive science for everyone.

clipkit • Rank 12.6 • Science 49%

a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

https://github.com/althonos/pyfamsa • Rank 12.2 • Science 49%

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

pycirclize • Rank 16.1 • Science 44%

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

data-management-resources • Rank 2.7 • Science 57%

Repo supporting the manuscript 'Journeying towards best practice data management in biodiversity genomics'.

orthofisher • Rank 10.2 • Science 49%

a broadly applicable tool for automated gene identification and retrieval

https://github.com/ay-lab/mustache • Rank 12.7 • Science 46%

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

hgvs • Rank 9.5 • Science 49%

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

sns • Rank 4.2 • Science 54%

Analysis pipelines for genomic sequencing data

pymsaviz • Rank 13.9 • Science 44%

MSA(Multiple Sequence Alignment) visualization python package for sequence analysis

pygenomeviz • Rank 13.8 • Science 44%

A genome visualization python package for comparative genomics

GSVA • Rank 21.8 • Science 36%

Gene set variation analysis

https://github.com/akikuno/dajin2 • Rank 8.7 • Science 49%

🔬 Genotyping tool for genome-edited samples using nanopore-targeted sequencing

recognizer • Rank 3.4 • Science 54%

A tool for domain based annotation with databases from the Conserved Domains Database

https://github.com/biojulia/popgen.jl • Rank 7.1 • Science 49%

Population Genetics in Julia

mungesumstats • Rank 7.0 • Science 49%

Rapid standardisation and quality control of GWAS or QTL summary statistics

https://github.com/althonos/pytantan • Rank 7.0 • Science 49%

Cython bindings and Python interface to Tantan, a fast method for identifying repeats in DNA and protein sequences.

https://github.com/althonos/diced • Rank 9.8 • Science 46%

A Rust reimplementation of the MinCED method for identifying CRISPRs in full or assembled genomes.

cpg-gnomad • Rank 19.6 • Science 36%

Hail helper functions for the gnomAD project and Translational Genomics Group

GenomicDataCommons • Rank 19.3 • Science 36%

Provide R access to the NCI Genomic Data Commons portal.

cerebra — Peer-reviewed • Rank 5.6 • Science 49%

cerebra: A tool for fast and accurate summarizing of variant calling format (VCF) files - Published in JOSS (2020)

gcmodeller • Rank 5.5 • Science 49%

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

gdsfmt • Rank 17.7 • Science 36%

R Interface to CoreArray Genomic Data Structure (GDS) Files (Development version only)

vcfR • Rank 17.2 • Science 36%

Tools to work with variant call format files

https://github.com/biocommons/bioutils • Rank 16.8 • Science 36%

provides common tools and lookup tables used primarily by the hgvs and uta packages

msigdbr • Rank 16.4 • Science 36%

MSigDB gene sets for multiple organisms in a tidy data format

cogclassifier • Rank 8.4 • Science 44%

A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category

pybarrnap • Rank 7.2 • Science 44%

Python implementation of barrnap (Bacterial ribosomal RNA predictor)

eutils • Rank 17.7 • Science 33%

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

ontoProc • Rank 14.6 • Science 36%