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

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

A friendly next-generation interface for Genomic data discovery powered by InterMine

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

Model and predict short DNA sequence features with neural networks

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

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

A powerful open source data warehouse system

Analysis pipelines for sequencing data

nim wrapper for htslib for parsing genomics data files

Official code repository for GATK versions 4 and up

Official git repository for Biopython (originally converted from CVS)

A list of web-based interactive biological data visualizations.

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

A versatile pairwise aligner for genomic and spliced nucleotide sequences

GenomeTools genome analysis system.

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

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)

Data intensive science for everyone.

A tool to circularize genome assemblies

Scalable genomic data analysis.

Chromosome visualization for the web

Scripts to download genomes from the NCBI FTP servers

NGLess: NGS with less work

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

Haplotype VCF comparison tools

C++ library and cmdline tools for parsing and manipulating VCF files

A cool place to store your Hi-C

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

Ten Quick Tips for Deep Learning in Biology

A fast and sensitive gapped read aligner

variant expressions, annotation, and filtering for great good.

Java utilities for Bioinformatics

SDK for GPU accelerated genome assembly and analysis

A comprehensive tutorial about GWAS and PRS

A collection of scripts and notes related to genomics and bioinformatics

A high-performance, Pythonic language for bioinformatics

Rapid large-scale prokaryote pan genome analysis

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

Antimicrobial Resistance Identification By Assembly

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

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

PHANOTATE: a tool to annotate phage genomes.

GCP Essentials for Bioinformatics Researchers

Detection of NCLDV signatures in 'omic data

An open-source toolkit for large-scale genomic analysis

De novo genome assembly and multisample variant calling

Genomics Extension for SQLite

Pan-genome wide association studies

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

Script to automatically create and run IGV snapshot batchscripts

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

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

Bayesian genotyper for structural variants