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                Bioinformatics Tools

Bioinformatics Tools

                        Bioinformatics Publications
          Database of Pharmacogenomic Information in Ethnic Minority Populations (dbPGxEMP)
          de novo Assembly Quality Evaluation Tool (dnAQET)
          FDALabel:  Full-Text Search of Drug Product Labeling


                        ArrayTrackTM HCA-PCA Standalone Package – powerful data-exploring tools
          Decision Forest
          Endocrine Disruptor Knowledge Base (EDKB)
          Estrogenic Activity Database (EADB)
          Liver Toxicity Knowledge Base (LTKB)
          MicroArray/Sequencing Quality Control (MAQC/SEQC)
          Mold2 Home
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          Bioinformatics Tools
          de novo Assembly Quality Evaluation Tool (dnAQET)Bioinformatics Tools de novo Assembly Quality Evaluation Tool (dnAQET)
  
  					dnAQET description, installation requirements, download instructions, and contact information for technical support
	
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The *de novo*Assembly Quality Evaluation Tool (dnAQET) is a framework designed to evaluate a *de novo*assembly along with its scaffolds/contigs against a trusted reference genome. It first generates a quality score for each scaffold of an assembly based on its length, the misassemblies observed in the alignments and the total alignment percentage of a scaffold. Based on the quality scores assigned to the contigs/scaffolds, it computes an overall quality score for the whole assembly.

Installation Requirements

The dnAQET is a Java package designed to be used in a Unix based operating system (such as Linux, MacOS, etc.) and it requires Java 1.7 Runtime Environment installed. It depends on Minimap2 tool and MUMmer4 package, which requires the following to run successfully.

perl5 (5.6.0)
	sh
	sed
	awkOn the other hand, the dnAQET package does not require any installation. It automatically compiles MUMmer or Minimap2 in the first use and the main jar file does not require any compilation or installation since it is in byte code designed to work in a Java RTE.

To Use dnAQET

Download the compressed file and extract it.
For more information and detailed instructions on how to use the dnAQET, please refer to the README file in the zip file.

Download the Tar.gz File for dnAQET (12.04 MB)

(*version 1.1*)

**NOTE:***This package was prepared with GNU tar and zipped with gzip utilities. Please directly use tar with -zxvf option to extract the contents of the package in a Linux-based operating system. If the package is extracted in a Windows system and the contents are transferred to a Linux based system, then the file system permissions of these files would be lost, which will result in malfunctioning of dnAQET software.*
	**Please contact**NCTRBioinformaticsSupport@fda.hhs.gov if you need assistance with accessing any documents contained inside the zip file.**


Contact Information

Functions
			Contacts*Questions, Suggestions, or Get Assistance:*
			Huixiao Hong (870-543-7296 or Huixiao.Hong@fda.hhs.gov)Resources For You

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                                                                                  Content current as of:
      08/17/2022
              
              
Topic(s)
			  Research
				    				       				    				       Toxicology
				       				    				       BioinformaticsBioinformatics Tools

          
                        Publications
          Database of Pharmacogenomic Information in Ethnic Minority Populations (dbPGxEMP)
          de novo Assembly Quality Evaluation Tool (dnAQET)
          FDALabel:  Full-Text Search of Drug Product Labeling


                        ArrayTrackTM HCA-PCA Standalone Package – powerful data-exploring tools
          Decision Forest
          Endocrine Disruptor Knowledge Base (EDKB)
          Estrogenic Activity Database (EADB)
          Liver Toxicity Knowledge Base (LTKB)
          MicroArray/Sequencing Quality Control (MAQC/SEQC)
          Mold2
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