1088 Open source projects that are alternatives of or similar to companion

GenomeTools genome analysis system.

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

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

annotate a VCF with other VCFs/BEDs/tabixed files

A package for designing compact and comprehensive capture probe sets.

A genome browser that shows long reads and complex variants better

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

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.

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

🔬 BEDOPS: high-performance genomic feature operations

Analysis pipelines for sequencing data

Data intensive science for everyone.

Official code repository for GATK versions 4 and up

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

Bayesian haplotype-based mutation calling

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Next generation sequencing reads de novo assembler.

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

A repository for setting up a RNAseq workflow

Rapid large-scale prokaryote pan genome analysis

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

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

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

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

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

Reads simulator

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

🔬 Assemble large genomes using short reads

nim wrapper for htslib for parsing genomics data files

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

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

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

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

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

Deep learning infrastructure for bioinformatics

Ten Quick Tips for Deep Learning in Biology

Intuitive local web frontend for the BLAST bioinformatics tool

A powerful open source data warehouse system

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Genome Annotation Without Nightmares

BACTpipe: An assembly and annotation pipeline for bacterial genomics

Haplotype VCF comparison tools

JavaScript VisualizationTools

Collection of scripts for bacterial genomics

Official git repository for Biopython (originally converted from CVS)

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

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

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

cython + htslib == fast VCF and BCF processing

De novo annotation of young retrotransposons

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

A faster lmm for GWAS. Supports GPU backend.

PERF is an Exhaustive Repeat Finder

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

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

Toolkit for preparing genomes for submission to NCBI

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.