569 Open source projects that are alternatives of or similar to Fermi2

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

An open-access bioinformatics text

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

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

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.

Toolkit for preparing genomes for submission to NCBI

A modern genome browser built with JavaScript and HTML5.

A package for designing compact and comprehensive capture probe sets.

Data intensive science for everyone.

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

Scalable genomic data analysis.

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

Official git repository for Biopython (originally converted from CVS)

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

Haplotype VCF comparison tools

The next version of bwa-mem

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

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

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

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

A curated list of awesome bioinformatics software.

Java utilities for Bioinformatics

A fast 23andMe genome text file parser, now superseded by arv

A comprehensive tutorial about GWAS and PRS

annotate a VCF with other VCFs/BEDs/tabixed files

cython + htslib == fast VCF and BCF processing

An open source platform for managing and analyzing biomedical big data

An ultrafast memory-efficient short read aligner

JavaScript VisualizationTools

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

A faster lmm for GWAS. Supports GPU backend.

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

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

🔬 BEDOPS: high-performance genomic feature operations

Fast hash function for DNA sequences

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

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

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

A fast and sensitive gapped read aligner

Compute N50/NG50 and auN/auNG

Bystro genetic analysis (annotation, filtering, statistics)

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

Ultra-fast and memory-efficient (meta-)genome assembler

Fast alignment and preprocessing of chromatin profiles

Predict plasmids from uncorrected long read data

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

Scripts to download genomes from the NCBI FTP servers

Earl Grey: A fully automated TE curation and annotation pipeline

De novo assembly based variant calling pipeline for Illumina short reads

Assembling the cause of phenotypes and genotypes from NGS data

Efficient pythonic random access to fasta subsequences

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A React web application to query and share any PostgreSQL database.

Example client programs for Saphetor's VarSome annotation API

A powerful open source data warehouse system

Intuitive local web frontend for the BLAST bioinformatics tool

Provide R access to the NCI Genomic Data Commons portal.

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

A high-performance, Pythonic language for bioinformatics

Tools to process and analyze deep sequencing data.