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

Assembling the cause of phenotypes and genotypes from NGS data

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

Bystro genetic analysis (annotation, filtering, statistics)

Multilocus sequence typing by blast using the schemes from PubMLST

Example client programs for Saphetor's VarSome annotation API

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

A modular annotation tool for genomic variants

Predict plasmids from uncorrected long read data

Toolkit for preparing genomes for submission to NCBI

Improve the quality of a denovo assembly by scaffolding and gap filling

Genome Annotation Without Nightmares

Earl Grey: A fully automated TE curation and annotation pipeline

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

Finds SNP sites from a multi-FASTA alignment file

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

Numerical Encoding for Human Genetic Variants

A tool to plot significant regions of GWAS

A bioinformatics pipeline to analyze mtDNA from NGS data

Spark VCF data source implementation for Dataframes

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

WebAssembly modules for genomics

A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Bioinformatics curated workflows that use Biocontainers tools

A fast, scalable, and accurate local ancestry method.

Identify phage regions in bacterial genomes for masking purposes

An R framework for phylostratigraphy

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

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

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

mgatk: mitochondrial genome analysis toolkit

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

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

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

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

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

Bioconductor package for management of multi-assay data

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

A package for designing activity-informed nucleic acid diagnostics for viruses.

Command line utility for manipulating Illumina-generated FastQ files.

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

Nextflow basic tutorial for newbie users

Python toolkit for building restartable pipelines

Python-based UCSC genome browser snapshot-taker and gallery-maker

Big Compute Learning Labs

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.

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

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.

A library for manipulating bioinformatics sequencing formats in Apache Spark

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

Distribution of TEs and their relationship to genes in host genome

Interactive assembly and analysis of RAD-seq data sets

Predict AMPs in (meta)genomes and peptides

Forward-time simulation in Python using fwdpp

Explore rearrangements and copy-number amplifications in a cancer genome