A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo ass...2606 days ago
CABOG: Celera Assembler with Best Overlap Graph
CABOG (Celera Assembler with Best Overlap Graph) is scientific software for DNA research. CABOG has been a critical component of many genome sequencing projects. C...2603 days ago
NCBI Prokaryotic Genome Annotation Pipeline
NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes an...ine that combines ab initio gene prediction algorithms with homology based m...2602 days ago
GAM-NGS: genomic assemblies merger for next generation sequencing
GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based p...2599 days ago
2598 days ago
SuRankCo: supervised ranking of contigs in de novo assemblies
SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs...2594 days ago
AVID: A Global Alignment Program
A new global alignment method called AVID. The method is designed to be fast, memory...ds for their comparison. These formats and methods should be useful for future studies. The tools we have developed...2594 days ago
Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA f...elp decide between alternative sequencing methods for a sequence-based p...2594 days ago
Synteny Portal: a web-based application portal for synteny block analysis
Synteny Portal, a versatile web-based application portal for constructing,...used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Sy...easily perform comparative genomics studies by compensating limitations o...2594 days ago
dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation
dbCAN is a web server and DataBase for automated Carb...;CAT. All data in dbCAN are generated based on the family classification... of the existing CAZyme families based on sequence similarities; db...Zy database created new families based o...2589 days ago