1287 Open source projects that are alternatives of or similar to catch

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

Official code repository for GATK versions 4 and up

Data intensive science for everyone.

UGENE is free open-source cross-platform bioinformatics software

A collection of scripts and notes related to genomics and bioinformatics

Analysis pipelines for sequencing data

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

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

NGLess: NGS with less work

Collection of scripts for bacterial genomics

Java utilities for Bioinformatics

An interactive web tool for quality control of DNA sequencing data

🌈Scaffold genome sequence assemblies using linked read sequencing data

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

🔬 Assemble large genomes using short reads

A genome browser that shows long reads and complex variants better

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

A repository for setting up a RNAseq workflow

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

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Assembling the cause of phenotypes and genotypes from NGS data

A fast 23andMe genome text file parser, now superseded by arv

Rapid large-scale prokaryote pan genome analysis

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

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

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

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

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

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

Genomics Extension for SQLite

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

Antimicrobial Resistance Identification By Assembly

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 tool to circularize genome assemblies

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Intuitive local web frontend for the BLAST bioinformatics tool

GenomeTools genome analysis system.

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

A curated list of awesome bioinformatics software.

Efficient pythonic random access to fasta subsequences

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

Tools to process and analyze deep sequencing data.

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

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

Official git repository for Biopython (originally converted from CVS)

Ultrafast sequence typing and gene detection from NGS raw reads

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Curated (meta)list of resources for Biology.

Data and analysis for the Splatter paper

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

🍺🔬 Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

Fast hash function for DNA sequences

An easy-to-use way for running Galaxy workflows.

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

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

Biopython Jupyter Notebook tutorial to characterize a small genome

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