961 Open source projects that are alternatives of or similar to gff3toembl

Assembling the cause of phenotypes and genotypes from NGS data

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

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

Multilocus sequence typing by blast using the schemes from PubMLST

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

Finds SNP sites from a multi-FASTA alignment file

Predict plasmids from uncorrected long read data

Rapid large-scale prokaryote pan genome analysis

A tool to circularize genome assemblies

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

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

Antimicrobial Resistance Identification By Assembly

Genomics Extension for SQLite

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

A collection of scripts and notes related to genomics and bioinformatics

Intuitive local web frontend for the BLAST bioinformatics tool

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

Official code repository for GATK versions 4 and up

Analysis pipelines for sequencing data

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

Data intensive science for everyone.

A package for designing compact and comprehensive capture probe sets.

An interactive web tool for quality control of DNA sequencing data

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

Bystro genetic analysis (annotation, filtering, statistics)

Earl Grey: A fully automated TE curation and annotation pipeline

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

🔬 BEDOPS: high-performance genomic feature operations

Proof-of-concept seq-to-graph mapper and graph generator

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.

An ultrafast memory-efficient short read aligner

A fast 23andMe genome text file parser, now superseded by arv

JavaScript VisualizationTools

Official git repository for Biopython (originally converted from CVS)

Haplotype VCF comparison tools

Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer

cython + htslib == fast VCF and BCF processing

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

De novo assembly based variant calling pipeline for Illumina short reads

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

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

Command line utility for manipulating Illumina-generated FastQ files.

Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)

BACNET is a Java based platform to develop website for multi-omics analysis

A modular annotation tool for genomic variants

A powerful open source data warehouse system

Collection of scripts for bacterial genomics

Tools for analyzing 10X Genomics data

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

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

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Toolkit for preparing genomes for submission to NCBI

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

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

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

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

Ploidy agnostic phasing pipeline and algorithm

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

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

Fast hash function for DNA sequences