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

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

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

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

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

Earl Grey: A fully automated TE curation and annotation pipeline

A powerful open source data warehouse system

A fast 23andMe genome text file parser, now superseded by arv

Haplotype VCF comparison tools

Fast hash function for DNA sequences

Toolkit for preparing genomes for submission to NCBI

Assembling the cause of phenotypes and genotypes from NGS data

Rapid large-scale prokaryote pan genome analysis

Reads simulator

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

Deep learning infrastructure for bioinformatics

A curated list of awesome bioinformatics software.

Official git repository for Biopython (originally converted from CVS)

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

🔬 BEDOPS: high-performance genomic feature operations

A faster lmm for GWAS. Supports GPU backend.

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

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

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

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Compute N50/NG50 and auN/auNG

Bystro genetic analysis (annotation, filtering, statistics)

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

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

Ten Quick Tips for Deep Learning in Biology

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

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

Intuitive local web frontend for the BLAST bioinformatics tool

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

cython + htslib == fast VCF and BCF processing

An ultrafast memory-efficient short read aligner

JavaScript VisualizationTools

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

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

A WGS de novo assembler based on the FMD-index for large genomes

A tool for fast and accurate summarizing of variant calling format (VCF) files

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Fast alignment and preprocessing of chromatin profiles

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

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

find large indels (in the blind spot between GATK/freebayes and SV callers)

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

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

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Provide R access to the NCI Genomic Data Commons portal.

A package for designing compact and comprehensive capture probe sets.

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

Complex structural variant detection from WGS data

nim wrapper for htslib for parsing genomics data files

Bayesian haplotype-based mutation calling

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

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

An open-access bioinformatics text

Predict plasmids from uncorrected long read data