579 Open source projects that are alternatives of or similar to fermikit

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

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

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

An open source platform for managing and analyzing biomedical big data

💾 📃 "Reads to report" for public health and clinical microbiology

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

Java utilities for Bioinformatics

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

Efficient pythonic random access to fasta subsequences

Scripts to download genomes from the NCBI FTP servers

Tools to process and analyze deep sequencing data.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

A collection of publications on comparison of high-throughput sequencing technologies.

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Official code repository for GATK versions 4 and up

Model and predict short DNA sequence features with neural networks

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

An interactive web tool for quality control of DNA sequencing data

Data intensive science for everyone.

A package for designing compact and comprehensive capture probe sets.

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

GCP Essentials for Bioinformatics Researchers

Bayesian genotyper for structural variants

A collection of scripts and notes related to genomics and bioinformatics

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Complex structural variant detection from WGS data

Official git repository for Biopython (originally converted from CVS)

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

Fast alignment and preprocessing of chromatin profiles

nim wrapper for htslib for parsing genomics data files

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

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

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

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

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

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

Deep learning infrastructure for bioinformatics

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

Ten Quick Tips for Deep Learning in Biology

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

Intuitive local web frontend for the BLAST bioinformatics tool

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

A tool to circularize genome assemblies

Haplotype VCF comparison tools

JavaScript VisualizationTools

xHLA: Fast and accurate HLA typing from short read sequence data

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

An ultrafast memory-efficient short read aligner

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

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

Predict plasmids from uncorrected long read data

Unsupervised domain adaptation method for relation extraction

A library to build and execute typed scientific workflows

3D printed sculpture of a DNA molecule, showing my own genome

Fast and flexible ORF finder

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

exploratory and interactive microbiome analyses based on heatmaps

Genetic Map Comparison