970 Open source projects that are alternatives of or similar to Bio.jl

Scripts to download genomes from the NCBI FTP servers

Official git repository for Biopython (originally converted from CVS)

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A modern genome browser built with JavaScript and HTML5.

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

A package for designing compact and comprehensive capture probe sets.

Ten Quick Tips for Deep Learning in Biology

A collection of scripts and notes related to genomics and bioinformatics

Java utilities for Bioinformatics

A fast 23andMe genome text file parser, now superseded by arv

An open-access bioinformatics text

Official code repository for GATK versions 4 and up

A powerful open source data warehouse system

Data intensive science for everyone.

Python and C++ code for reading and writing genomics data.

Efficient pythonic random access to fasta subsequences

Analysis pipelines for sequencing data

A curated list of awesome bioinformatics software.

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

Intuitive local web frontend for the BLAST bioinformatics tool

Proof-of-concept seq-to-graph mapper and graph generator

cython + htslib == fast VCF and BCF processing

🔬 BEDOPS: high-performance genomic feature operations

De novo assembly based variant calling pipeline for Illumina short reads

BACNET is a Java based platform to develop website for multi-omics analysis

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

GenomeTools genome analysis system.

Numerical Encoding for Human Genetic Variants

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

A genome browser that shows long reads and complex variants better

An ultrafast memory-efficient short read aligner

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

Deep learning infrastructure for bioinformatics

A faster lmm for GWAS. Supports GPU backend.

Ultrafast sequence typing and gene detection from NGS raw reads

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Predict AMPs in (meta)genomes and peptides

Haplotype VCF comparison tools

A simple command-line tool to download data from Joint Genome Institute databases

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

JavaScript VisualizationTools

Binomica Public Repository for Biological Parts

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Example client programs for Saphetor's VarSome annotation API

Simple pure Python SAM parser and objects for working with SAM records

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

Fast hash function for DNA sequences

dysgu-SV is a collection of tools for calling structural variants using short or long reads

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

DOM Text Based Multiple Sequence Alignment Library

Earl Grey: A fully automated TE curation and annotation pipeline

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

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

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Compute N50/NG50 and auN/auNG

Bystro genetic analysis (annotation, filtering, statistics)

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Provide R access to the NCI Genomic Data Commons portal.

Assembling the cause of phenotypes and genotypes from NGS data