275 Open source projects that are alternatives of or similar to fermi

De novo assembly based variant calling pipeline for Illumina short reads

Deep learning infrastructure for bioinformatics

MISO: An open-source LIMS for NGS sequencing centres

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

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

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

Code examples of fast and simple k-mer counters for tutorial purposes

🔬 BEDOPS: high-performance genomic feature operations

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Simulate genealogical trees and genomic sequence data using population genetic models

AQUAS TF and histone ChIP-seq pipeline

A curated list of bioinformatics bench-marking papers and resources.

Intuitive local web frontend for the BLAST bioinformatics tool

Bayesian haplotype-based mutation calling

Performant Pythonic GenomicRanges

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

A genome browser that shows long reads and complex variants better

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

cython + htslib == fast VCF and BCF processing

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Reads simulator

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Fast large scale matrix visualization for the web.

Viral genomics analysis pipelines

Bioinformatics library for .NET

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

Genomic Data Retrieval with R

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

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

A Java API for high-throughput sequencing data (HTS) formats.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A powerful open source data warehouse system

nim wrapper for htslib for parsing genomics data files

Official git repository for Biopython (originally converted from CVS)

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

GenomeTools genome analysis system.

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

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

A tool to circularize genome assemblies

Chromosome visualization for the web

NGLess: NGS with less work

Haplotype VCF comparison tools

A cool place to store your Hi-C

Ten Quick Tips for Deep Learning in Biology

variant expressions, annotation, and filtering for great good.

SDK for GPU accelerated genome assembly and analysis

A collection of scripts and notes related to genomics and bioinformatics

Rapid large-scale prokaryote pan genome analysis

Antimicrobial Resistance Identification By Assembly

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

GCP Essentials for Bioinformatics Researchers

An open-source toolkit for large-scale genomic analysis

Genomics Extension for SQLite

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

Script to automatically create and run IGV snapshot batchscripts

Tools to work with variant call format files

A DNA Sequence Alignment/Map (SAM) library for Clojure

JavaScript VisualizationTools

An ultrafast memory-efficient short read aligner

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