Software


decontaMiner

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Next Generation Sequencing (NGS) experiments produce millions of short sequences that, mapped to a reference genome, provide biological insights at genomic, transcriptomic and epigenomic level. Nonetheless, a variable number of reads fails to correctly align to the reference. In most of the cases this failure is due to the low quality of the bases called […]

HvDBase

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The Whole Transcriptome Shotgun Sequencing (RNA-seq) uses the Next Generation Sequencing (NGS) capabilities to analyze RNA transcript counts and their quanti cation, with an extraordinary accuracy. In order to provide a comprehensive knowledge about the non-reference model organism Hydra vulgaris water polyp, we developed a comprehensive database in which the whole functional annotated transcriptome is integrated, […]

TRANSCRIPTATOR 2.0

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RNA-Seq is a new tool, which utilizes high-throughput sequencing to measure RNA transcript counts at an extraordinary accuracy. It provides quantitative means to explore the transcriptome of an organism of interest. However, interpreting this extremely large data coming out from RNA-Seq into biological knowledge is a problem, and biologist-friendly tools to analyze them are lacking. […]

OPENDoRM

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OPENDoRM (Optimization of Pooled Experiments in NGS for Detection of Rare Mutations) is a freely available web resource with a Graphical User Interface (GUI) for planning of NGS experiments. It provides flexibility to the users for automatically carrying out analysis in terms of costs associated with the optimal allocation of patients in pools. Users are […]

Lims

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A Laboratory Information Management System (LIMS), is a software-based laboratory and information management systemthat offers a set of key features that support a modern laboratory’s operations. Why we need LIMS?  •  With advent of High through put technologies large amount of data •  Quality and quantity of information is increasing exponentially •  Large amount of […]

MetaboX

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We release the MetaboX library, an open source PHP framework for developing metabolic networks from a set of compounds. This library provides easy access to the Kyoto Encyclopedia for Genes and Genomes (KEGG) database using its RESTful Application Programming Interfaces (APIs), and methods to enhance manipulation of the information returned from KEGG webservice. MetaboX includes […]