293 Open source projects that are alternatives of or similar to TOGA

A fast, scalable, and accurate local ancestry method.

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

Identify phage regions in bacterial genomes for masking purposes

ntHash implementation in Rust

An R framework for phylostratigraphy

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

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

GA4GH Variation Representation Python Implementation

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

use the noise

mgatk: mitochondrial genome analysis toolkit

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Predict AMPs in (meta)genomes and peptides

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

Forward-time simulation in Python using fwdpp

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

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Transcripts annotation and GO enrichment Fisher tests

Tools for analyzing 10X Genomics data

Collection of scripts for bacterial genomics

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

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Phage-Host Interaction Search Tool

Bioconductor package for management of multi-assay data

High-performance error correction for Illumina resequencing data

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Easy genetic ancestry predictions in Python

Nextflow basic tutorial for newbie users

Python package and CLI for whole-genome duplication related analyses

Python toolkit for building restartable pipelines

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Big Compute Learning Labs

Genomics Workflows on AWS

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

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

A library for manipulating bioinformatics sequencing formats in Apache Spark

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

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

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

Haplotype VCF comparison tools

Interactive assembly and analysis of RAD-seq data sets

phenol: Phenotype ontology library

Official git repository for Biopython (originally converted from CVS)

A DNA Sequence Alignment/Map (SAM) library for Clojure

Explore rearrangements and copy-number amplifications in a cancer genome

JavaScript VisualizationTools

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

cython + htslib == fast VCF and BCF processing

Bead-based single-cell atac processing

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

An ultrafast memory-efficient short read aligner

Resource of human chromosome schematics & images

🐳 Bio-dockers: dockerized bioinformatic tools

Explore gnomAD datasets on the web

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

Performant Pythonic GenomicRanges

GREIN : GEO RNA-seq Experiments Interactive Navigator