325 Open source projects that are alternatives of or similar to cerebra

De novo assembly based variant calling pipeline for Illumina short reads

Clustering scRNAseq by genotypes

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

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

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

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

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

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

Complex structural variant detection from WGS data

De novo genome assembly and multisample variant calling

JavaScript VisualizationTools

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

A genome browser that shows long reads and complex variants better

Deep learning infrastructure for bioinformatics

Discover differential transcript usage from polyA-captured single cell RNA-seq data

cython + htslib == fast VCF and BCF processing

Reads simulator

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

An ultrafast memory-efficient short read aligner

Viral genomics analysis pipelines

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

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

Build React forms based on GraphQL APIs.

Performant Pythonic GenomicRanges

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

A powerful open source data warehouse system

Haplotype VCF comparison tools

GenomeTools genome analysis system.

Seven Bridges Genomics aligner/caller debugging and analysis tools

Chromosome visualization for the web

Official git repository for Biopython (originally converted from CVS)

Ten Quick Tips for Deep Learning in Biology

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

Rapid large-scale prokaryote pan genome analysis

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

An open-source toolkit for large-scale genomic analysis

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

Tools to work with variant call format files

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

Genomic Data Retrieval with R

🔬 BEDOPS: high-performance genomic feature operations

Bayesian haplotype-based mutation calling

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

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

nim wrapper for htslib for parsing genomics data files

SDK for GPU accelerated genome assembly and analysis

MISO: An open-source LIMS for NGS sequencing centres

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

Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).

Indigo: SNV and InDel Discovery in Chromatogram traces obtained from Sanger sequencing of PCR products

Fast large scale matrix visualization for the web.

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

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

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

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

A tool to circularize genome assemblies

Clone identification from single-cell data