569 Open source projects that are alternatives of or similar to Smudgeplot

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

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

Efficient pythonic random access to fasta subsequences

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

A fast 23andMe genome text file parser, now superseded by arv

A cool place to store your Hi-C

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

A tool to circularize genome assemblies

A collection of scripts and notes related to genomics and bioinformatics

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

Bayesian haplotype-based mutation calling

Fast alignment and preprocessing of chromatin profiles

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`

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

GenomeTools genome analysis system.

Genomics Extension for SQLite

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

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

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

cython + htslib == fast VCF and BCF processing

🔬 BEDOPS: high-performance genomic feature operations

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

Haplotype VCF comparison tools

Antimicrobial Resistance Identification By Assembly

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

Fast hash function for DNA sequences

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

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

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

Bystro genetic analysis (annotation, filtering, statistics)

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

Provide R access to the NCI Genomic Data Commons portal.

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

Toolkit for preparing genomes for submission to NCBI

annotate a VCF with other VCFs/BEDs/tabixed files

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

Python and C++ code for reading and writing genomics data.

Analysis pipelines for sequencing data

Lightweight Iterative Gene set Enrichment in R

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

Tools and databases for analyzing HLA and VDJ genes.

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

igv.js server and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).

RADseq Data Exploration, Manipulation and Visualization using R

Race and ethnicity Imputation from Disease history with Deep LEarning

Post-analysis of immune repertoire sequencing data

Robust and efficient workflows using a simple language agnostic approach

A list of web-based interactive biological data visualizations.

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

The START App: R Shiny Transcriptome Analysis Resource Tool

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Create regional association plots from GWAS or meta-analysis