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Annotation pipeline software tools | Genome annotation

DNA sequence annotation consists in several successive steps, including location of coding and non-coding sequences, gene prediction, identification of regulatory elements and functional annotation. Genome annotation pipelines are proposing a suite…
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Orione
Web

Orione

A Galaxy-based framework consisting of publicly available research software and…

A Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology…

MicroScope
Web

MicroScope

Supports systematic and efficient revision of microbial genome annotation, data…

Supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. MicroScope allows users to analyze microbial (meta)genomes together with…

Orcae
Dataset

Orcae

Offers public access to a wide variety of plant, fungal and animal genomes.…

Offers public access to a wide variety of plant, fungal and animal genomes. ORCAE is a wikistyle annotation portal. The basic setup of this tool is highly comparable to wiki systems such as…

Pse-Analysis
Desktop

Pse-Analysis

Expedites the pace in conducting genome/proteome analysis. Pse-Analysis can…

Expedites the pace in conducting genome/proteome analysis. Pse-Analysis can automatically complete the following five procedures: (1) sample feature extraction, (2) optimal parameter selection, (3)…

FARAO
Desktop

FARAO Flexible All-Round Annotation Organizer

A set of software tools that constitute as a highly configurable way to handle…

A set of software tools that constitute as a highly configurable way to handle sequence annotation and coverage information. FARAO 1) integrates annotation and coverage information for the same…

ConsPred
Desktop

ConsPred

A prokaryotic genome annotation framework that performs intrinsic gene…

A prokaryotic genome annotation framework that performs intrinsic gene predictions, homology searches, predictions of non-coding genes as well as CRISPR repeats and integrates all evidence into a…

P-CAPS
Desktop

P-CAPS Prokaryotic Contigs Annotation Pipeline Server

Performs genome prediction and annotation on prokaryotic genomic sequence.…

Performs genome prediction and annotation on prokaryotic genomic sequence. P-CAPS integrates publicly programs into a server application. This tool can be installed on any platform and provides the…

DanQ
Desktop

DanQ

A hybrid convolutional and bi-directional long short-term memory recurrent…

A hybrid convolutional and bi-directional long short-term memory recurrent neural network framework for predicting non-coding function de novo from sequence. In the DanQ model, the convolution layer…

Companion
Web
Desktop

Companion COMprehensive Parasite ANnotatION

A web server providing parasite genome annotation as a service using a…

A web server providing parasite genome annotation as a service using a reference-based approach. Companion delivers a readily usable annotation of features in the target genome, in a variety of…

ANNOgesic
Desktop

ANNOgesic

Uses for the analysis of bacterial RNA-Seq data. ANNOgesic is a modular,…

Uses for the analysis of bacterial RNA-Seq data. ANNOgesic is a modular, user-friendly annotation pipeline that integrates different types of data like dRNA-Seq as well as RNA-Seq generated after…

G T A T C G C T A
DeNoGAP
Desktop

DeNoGAP De-Novo Genome Analysis Pipeline

Performs reference-assisted and de novo gene prediction, homolog protein family…

Performs reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis. DeNoGAP integrates bioinformatics…

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lncRNA-screen
Desktop

lncRNA-screen

A comprehensive pipeline for computationally screening putative long non-coding…

A comprehensive pipeline for computationally screening putative long non-coding RNA (lncRNA) transcripts over large multimodal datasets. lncRNA-screen main objective is to facilitate the…

G T A T C G C T A
VAX
Desktop

VAX Variant Annotator eXtras

A scalable method for using the plugin capability of the Ensembl Variant Effect…

A scalable method for using the plugin capability of the Ensembl Variant Effect Predictor to enrich its basic set of variant annotations with additional data on genes, function, conservation,…

BlastKOALA
Web

BlastKOALA

Assigns K numbers to the user's sequence data by BLAST searches,…

Assigns K numbers to the user's sequence data by BLAST searches, respectively, against a nonredundant set of KEGG GENES. KOALA (KEGG Orthology And Links Annotation) is KEGG's internal…

RAST
Web

RAST Rapid Annotation using Subsystem Technology

An automatic annotation server for microbial genomes, built upon the framework…

An automatic annotation server for microbial genomes, built upon the framework provided by the SEED system. A new user must register for the service, which involves giving us contact information and…

BG7
Desktop

BG7

An open source bacterial genome annotation system, specifically designed for…

An open source bacterial genome annotation system, specifically designed for NGS data. BG7 is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or…

FunGAP
Desktop

FunGAP

Predicts protein-coding genes in a fungal genome assembly. FunGAP comprises…

Predicts protein-coding genes in a fungal genome assembly. FunGAP comprises three major steps: (i) preprocessing, (ii) gene prediction and (iii) evaluation and filtration. This tool evaluates…

GC-Specific…
Desktop

GC-Specific MAKER

Predicts new and improved gene models and assesses the biological significance…

Predicts new and improved gene models and assesses the biological significance of this method in Oryza sativa. GC-specific MAKER is an annotation protocol that makes use of genes with high and low GC…

AnnBuilder
Desktop

AnnBuilder

Provides parsers to process annotation data from LocusLink, Gene Ontology…

Provides parsers to process annotation data from LocusLink, Gene Ontology Consortium, and Human Gene Project and can be extended to new data sources via user defined parsers. AnnBuilder is an R…

synbreed
Desktop

synbreed

Derives genome-based predictions from high-throughput genotyping and…

Derives genome-based predictions from high-throughput genotyping and large-scale phenotyping data. synbreed contains a comprehensive collection of functions required to fit and cross-validate genomic…

NPACT
Desktop
Web

NPACT N-Profile Analysis Computational Tool

A computational and graphical representation tool for gene identification and…

A computational and graphical representation tool for gene identification and sequence annotation. NPACT identifies sequence segments of any length with statistically-significant 3-base compositional…

G T A T C G C T A
BUSCO
Desktop

BUSCO Benchmarking Universal Single-Copy Orthologs

Provides measures for quantitative assessment of genome assembly, gene set, and…

Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal…

G T A T C G C T A
IonGAP
Web

IonGAP

A publicly available web platform designed for the analysis of whole bacterial…

A publicly available web platform designed for the analysis of whole bacterial genomes by using Ion Torrent sequence data. Besides assembly, IonGAP integrates a variety of comparative genomics,…

DIYA
Desktop

DIYA Do-It-Yourself Annotator

A modular and configurable open source pipeline software, written in Perl, used…

A modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. DIYA is currently used to take DNA contigs as input, either in…

Genix
Desktop

Genix

Provides a more reliable annotation of both protein-coding and non-coding…

Provides a more reliable annotation of both protein-coding and non-coding genes. Genix is an automated pipeline for bacterial genome annotation. This server performs the annotations one-by-one, so…

CEGMA
Desktop

CEGMA Core Eukaryotic Genes Mapping Approach

A computational method for building a highly reliable set of gene annotations…

A computational method for building a highly reliable set of gene annotations in the absence of experimental data. CEGMA includes the use of profile-hidden Markov models to ensure the reliability of…

Dintor
Desktop

Dintor

Provides a set of over 30 tools to assist researchers in the exploration of…

Provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets. Dintor covers a wide range of frequently required functionalities, from gene identifier…

BEACON
Desktop
Web

BEACON Bacterial GEnome Annotation ComparisON

A fast tool for an automated and a systematic comparison of different…

A fast tool for an automated and a systematic comparison of different annotations of single genomes. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained…

GASS
Desktop

GASS Genome Annotation based on Species Similarity

A fast and easy-to-use computational tool to annotate a eukaryotic genome based…

A fast and easy-to-use computational tool to annotate a eukaryotic genome based on only the annotations from another similar species. Based on the alignments from the exons’ sequences of annotated…

MAKER-P
Desktop

MAKER-P

Makes the annotation of novel plant genomes tractable for small groups with…

Makes the annotation of novel plant genomes tractable for small groups with limited bioinformatics experience and resources, and faster and more transparent for large groups with more experience and…

FLAN
Web

FLAN FLu ANnotation

Automatically annotates genomes of influenza virus A and B based on existing…

Automatically annotates genomes of influenza virus A and B based on existing protein sequences in GenBank. For each segment, a set of sample protein sequences is maintained on the server. A special…

KAAS
Web

KAAS KEGG Automatic Annotation Server

Automatically assigns K numbers to genes in the genome, enabling reconstruction…

Automatically assigns K numbers to genes in the genome, enabling reconstruction of KEGG pathways and BRITE hierarchies. The method is based on sequence similarities, bi-directional best hit…

AGMIAL
Desktop

AGMIAL

An integrated system for bacterial genome annotation. AGMIAL has been developed…

An integrated system for bacterial genome annotation. AGMIAL has been developed with the following requirements in mind: maximize annotation automation, ability to work on draft sequences, keep the…

AMIGene
Web

AMIGene Annotation of MIcrobial Genes

An application for automatically identifying the most likely coding sequences…

An application for automatically identifying the most likely coding sequences (CDSs) in a large contig or a complete bacterial genome sequence. The first step in AMIGene is dedicated to the…

MaGe
Web

MaGe Magnifying Genomes

A microbial genome annotation system based on a relational database containing…

A microbial genome annotation system based on a relational database containing information on bacterial genomes, as well as a web interface to achieve genome annotation projects. This system allows…

MICheck
Web

MICheck MIcrobial genome Checker

Enables rapid verification of sets of annotated genes and frameshifts in…

Enables rapid verification of sets of annotated genes and frameshifts in previously published bacterial genomes. The web interface allows one easily to investigate the MICheck results, i.e.…

BASys
Web

BASys Bacterial Annotation System

A web server that performs automated, in-depth annotation of bacterial genomic…

A web server that performs automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences. BASys uses more than 30 programs to determine nearly 60 annotation subfields for…

PGAP
Web

PGAP Prokaryotic Genome Annotation Pipeline

An automatic prokaryotic genome annotation pipeline that combines ab initio…

An automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. Combining the best features of the pan-genome approach in highly…

EvidentialGene
Desktop

EvidentialGene

Improves the annotation of the N. vitripennis genome, by increasing the gene…

Improves the annotation of the N. vitripennis genome, by increasing the gene count, reducing the number of missing genes and providing more comprehensive data on splicing and gene structure.…

EuGene-PP
Desktop

EuGene-PP

A fully automated pipeline for structural annotation of prokaryotic genomes…

A fully automated pipeline for structural annotation of prokaryotic genomes integrating protein similarities, statistical information and any oriented expression information (RNA-seq or tiling…

Prokka
Desktop

Prokka

A command line software tool to fully annotate a draft bacterial genome in…

A command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in…

Sma3s
Desktop

Sma3s Sequence massive annotator using 3 modules

An easy-to-use tool for high throughput annotation that provides both accuracy…

An easy-to-use tool for high throughput annotation that provides both accuracy and broad applicability for different kinds of sequence datasets. It is especially focused on the massive annotation of…

MEGANTE
Web

MEGANTE

An easy-to-use web service for integrated genome annotation. MEGANTE has a…

An easy-to-use web service for integrated genome annotation. MEGANTE has a simple interface to submit query sequences and performs genome annotation including repeat masking, transcript and protein…

Genome…
Web

Genome Sequence Annotation Server

Provides a pipeline for whole genome structural and functional annotation.…

Provides a pipeline for whole genome structural and functional annotation. GenSAS is web-based interface which guides researchers through the annotation process from start to finish and integrates…

GenDBE
Web

GenDBE

Automatically identifies, classifies and annotates genes using a large…

Automatically identifies, classifies and annotates genes using a large collection of software tools. GenDBE offers user interfaces that allow expert annotation with large, geo-graphically dispersed…

BIRAP
Desktop

BIRAP Bacterial Intergenic Region Analysis Pipeline

An open source, easy to use Perl pipeline that can be used to re-annotate…

An open source, easy to use Perl pipeline that can be used to re-annotate bacterial genomes using experimental data. The tool integrates expression profile derived from RNA-seq and/or proteogenomics,…

SHAP
Desktop

SHAP Simple High-throughput Annotation Pipeline

A lightweight and scalable sequence annotation pipeline capable of supporting…

A lightweight and scalable sequence annotation pipeline capable of supporting research efforts that generate or utilize large volumes of DNA sequence data. SHAP provides Grid capable analysis,…

GenoQuery
Desktop

GenoQuery

A module for querying a relational genomic warehouse. GenoQuery is based on an…

A module for querying a relational genomic warehouse. GenoQuery is based on an original multi-layer architecture of the warehouse, made of two layers, the entities layer and the databases layer. One…

OMIGA
Desktop

OMIGA Optimized Maker-based Insect Genome Annotation

A pipeline to predict protein-coding genes from insect genomes. The OMIGA…

A pipeline to predict protein-coding genes from insect genomes. The OMIGA pipeline was used to annotate the draft genome of an important insect pest, Chilo suppressalis, yielding 12,548 genes.…

TriAnnot
Web

TriAnnot

A versatile, easy-to-use online automated tool for annotation of large and…

A versatile, easy-to-use online automated tool for annotation of large and complex genomes. Its modular architecture allows for the annotation and masking of transposable elements, the structural,…

GATU
Desktop

GATU Genome Annotation Transfer Utility

Transfers annotations from a reference genome to a closely related target…

Transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU detects open reading frames…

G T A T C G C T A
FastAnnotator
Web

FastAnnotator

Assigns functional annotations. FastAnnotator efficiently annotates sequences…

Assigns functional annotations. FastAnnotator efficiently annotates sequences with their gene functions, enzyme functions or domains. It is useful in transcriptome studies and especially for those…

EuCAP
Desktop

EuCAP Eukaryotic Community Annotation Package

Incorporates structural and functional annotation from the community into an…

Incorporates structural and functional annotation from the community into an on-going annotation effort. EuCAP integrates the community annotators (CA) annotation in the current project annotation…

AGeS
Desktop

AGeS Annotation of microbial Genome Sequences

Incorporates publicly available and in-house-developed bioinformatics tools and…

Incorporates publicly available and in-house-developed bioinformatics tools and databases for integrated high-throughput genome annotation and protein function prediction. AGeS was designed to…

STINGRAY
Web
Desktop

STINGRAY System for Integrate Genomic Resources and Analyses

Offers a complete annotation pipeline for integrating, analyzing, annotating…

Offers a complete annotation pipeline for integrating, analyzing, annotating and presenting genomic and expression data from sequencing platforms. STINGRAY offers to user a phylogenetic module that…

MAKER
Web
Desktop

MAKER

A portable and easily configurable genome annotation pipeline. MAKER allows…

A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.…

G-OnRamp
Web
Desktop

G-OnRamp

Combines two successful and long-running projects—the Genomics Education…

Combines two successful and long-running projects—the Genomics Education Partnership (GEP) and the Galaxy Project. G-OnRamp aims to create an integrated, web-based, and scalable environment that…

G T A T C G C T A
transPLANT
Web

transPLANT

A plant informatics infrastructure. transPLANT is a virtualization platform,…

A plant informatics infrastructure. transPLANT is a virtualization platform, that provides access to specific genomic applications and workflows. transPLANT develops integrated standards and…

Franklin
Desktop

Franklin

A DNA sequence annotation tool built in order to play with SVGs, React, and…

A DNA sequence annotation tool built in order to play with SVGs, React, and Redux. Franklin is an SVG-based application to export annotated sequence as an image that can be further integrated in a…

RAPYD
Web

RAPYD Rapid Annotation Platform for Yeast Data

Connects universal genome analysis and interpretation methods. RAPYD supports…

Connects universal genome analysis and interpretation methods. RAPYD supports the understanding of yeast specific features, its lifestyle, and metabolic blue-prints by applying and combining…

ISGA
Web

ISGA Integrative Services for Genomics Analysis

A web-based prokaryotic genome annotation server, which builds upon the Ergatis…

A web-based prokaryotic genome annotation server, which builds upon the Ergatis workflow system, integrates other dynamic analysis tools and provides intuitive web interfaces for biologists to…

GI-POP
Web

GI-POP

A comprehensive annotation web server designed for ongoing genome project…

A comprehensive annotation web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible genomic islands (GIs),…

WeGAS
Web

WeGAS Web based microbial Genome Annotation System

Provides features that include gene prediction, homology search, promoter/motif…

Provides features that include gene prediction, homology search, promoter/motif analysis, genome browsing, gene ontology analysis based on the COGs and GO, and metabolic pathway analysis with…

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