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. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).
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 one to initiate the annotation of a genome at the early stage of the finishing phase. MaGe's main features are (i) integration of annotation data from bacterial genomes enhanced by a gene coding re-annotation process using accurate gene models, (ii) integration of results obtained with a wide range of bioinformatics methods, among which exploration of gene context by searching for conserved synteny and reconstruction of metabolic pathways, (iii) an advanced web interface allowing multiple users to refine the automatic assignment of gene product functions.
Helps in genome annotation. RATT is a software that allows users to transfer any entries from a reference sequence to similar samples. It can be applied to successive versions of a genome assembly, genomes of closely related species or strains. In addition, the software is also able to detect dissimilarities between two sequences and to generate inputs making genomes’ features to be visualized with Artemis. The software is a part of PAGIT toolkit.
Provides the workflow used to obtain whole-genome sequence data of 340 sequence type (ST) 772 Staphylococcus aureus isolates (the Bengal Bay clone). bengal-bay allows users to reproduce core analyses, including parameter settings, cluster resource configurations and versioned software distributions. The workflow implements Anaconda virtual environments, including software distributed in the Bioconda channel and is executable through Snakemake.
Aims to support real-time infectious disease outbreak investigations and pathogen surveillance using genomic data. IRIDA is a platform for analytics and visualizations of whole genome sequencing (WGS)-based microbial pathogen investigations that: (1) allows data management and controlled, collaborative data sharing, (2) provides analysis pipelines for public health genomics, enables data integration by implementing ontologies, and (3) permits data visualization.
Follows the annotation graph approach, offering a unified graph-based representation. GenomeTools is a software library and an associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. To process large annotation sets with low memory overhead, the tool has been designed and implemented as an pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations.
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 program modular and extensible, choose informatics and bioinformatics standards when possible (e.g. Web Services, RDBMS, ...), distribute the program under an open-source license.