305 Open source projects that are alternatives of or similar to Ideogram

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

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

AQUAS TF and histone ChIP-seq pipeline

Training and evaluating a variational autoencoder for pan-cancer gene expression data

Bayesian genotyper for structural variants

Simulate genealogical trees and genomic sequence data using population genetic models

nim wrapper for htslib for parsing genomics data files

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

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

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

An ensemble approach to accurately detect somatic mutations using SomaticSeq

Development repository for the Bioconductor package 'mixOmics '

variant expressions, annotation, and filtering for great good.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Tools to work with variant call format files

Bioinformatics library for .NET

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

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

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

An interactive web tool for quality control of DNA sequencing data

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

A collaboratively written review paper on deep learning, genomics, and precision medicine

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

Framework for building fast genomics web tools with WebAssembly and WebWorkers

NGLess: NGS with less work

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

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

Microassembly based somatic variant caller for NGS data

microsatellite instability detection using tumor only or paired tumor-normal data

Viral genomics analysis pipelines

A collection of scripts and notes related to genomics and bioinformatics

Bayesian haplotype-based mutation calling

Antimicrobial Resistance Identification By Assembly

Rapid large-scale prokaryote pan genome analysis

GCP Essentials for Bioinformatics Researchers

MISO: An open-source LIMS for NGS sequencing centres

Genomics Extension for SQLite

Lollipop-style mutation diagrams for annotating genetic variations.

Script to automatically create and run IGV snapshot batchscripts

Pan-genome wide association studies

Ten Quick Tips for Deep Learning in Biology

A fast whole-genome aligner based on de Bruijn graphs

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

Flexible genotype query among 30,000+ samples whole-genome

Genomic Data Retrieval with R

A friendly next-generation interface for Genomic data discovery powered by InterMine

A tool to circularize genome assemblies

Model and predict short DNA sequence features with neural networks

Personal Cancer Genome Reporter (PCGR)

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

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

identifying mutational significance in cancer genomes

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

Guided synteny alignment between duplicated genomes (within specified quota constraint)

An R package for creating Q-Q and manhattan plots from GWAS results

Deep learning infrastructure for bioinformatics

Reads simulator

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