Most popular bioinformatics repositories and open source projects

bioinfo-notebook

🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with...

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genome_updater

Bash script to download/update snapshots of files from NCBI genomes re...

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RNAlysis

RNA sequencing analysis software

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bionitio

Demonstrating best practices for bioinformatics command line tools

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dockstore

Our VM/Docker sharing infrastructure and management component

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GeneFuse

Gene fusion detection and visualization

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PhysiCell

PhysiCell: Scientist end users should use latest release! Developers p...

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spacegraphcats

Indexing & querying large assembly graphs -- in space, no one can hear...

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plass

Protein-Level ASSembler (PLASS): sensitive and precise protein assembl...

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UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena plat...

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fermikit

De novo assembly based variant calling pipeline for Illumina short rea...

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saber

Saber is a deep-learning based tool for information extraction in the...

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swarm

A robust and fast clustering method for amplicon-based studies

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gencore

Generate duplex/single consensus reads to reduce sequencing noises and...

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dbsnp

dbSNP

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biocypher

A unifying framework for biomedical research knowledge graphs

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mygene.info

MyGene.info: A BioThings API for gene annotations

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biojava-tutorial

:book::books:An introductory tutorial for BioJava

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SNPRelate

R package: parallel computing toolset for relatedness and principal co...

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fastqp

Simple FASTQ quality assessment using Python

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molgenis

MOLGENIS - for scientific data: management, exploration, integration a...

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fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes...

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cLoops

Accurate and flexible loops calling tool for 3D genomic data.

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biojupies

Automated generation of tailored bioinformatics Jupyter Notebooks via...

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Clair

Clair: Exploring the limit of using deep neural network on pileup data...

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bio-transformers

bio-transformers is a wrapper on top of the ESM/Protbert model, traine...

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redundans

Redundans is a pipeline that assists an assembly of heterozygous/polym...

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dolphinnext

A graphical user interface for distributed data processing of high thr...

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swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visuali...

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BioFSharp

Open source bioinformatics and computational biology toolbox written i...

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hAMRonization

Parse multiple Antimicrobial Resistance Analysis Reports into a common...

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nightingale

Data visualisation web components for the life sciences.

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best

Bam Error Stats Tool (best): analysis of error types in aligned reads.

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perbase

Per-base per-nucleotide depth analysis

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DEEPScreen

DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks...

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deepsignal

Detecting methylation using signal-level features from Nanopore sequen...

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grabseqs

A utility for easy downloading of reads from next-gen sequencing repos...

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GenomicConsensus

PacBio® variant and consensus caller

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block-aligner

SIMD-accelerated library for computing global and X-drop affine gap pe...

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strobealign

Aligns short reads using dynamic seed size with strobemers

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chewBBACA

BSR-Based Allele Calling Algorithm

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Terpene-Profile-Parser-for-Cannabis-Strains

Parser and database to index the terpene profile of different strains...

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Plant-Disease-Identification-using-CNN

Plant Disease Identification Using Convulutional Neural Network

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NucleoATAC

nucleosome calling using ATAC-seq

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ga4gh-server

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED...

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eager

A fully reproducible and state-of-the-art ancient DNA analysis pipelin...

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cute-nucleotides

Cute tricks for SIMD vectorized binary encoding and decoding of nucleo...

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pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for ge...

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philosopher

A complete toolkit for shotgun proteomics data analysis

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RNArtist

RNArtist allows you to design and paint your RNA 2D structures interac...

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