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GAGE analysis (Galaxy tool version 0.2)

Reference genome file in FASTA format:

Contig file in FASTA format:

Scaffold file in FASTA format:

What it does

This Galaxy tool uses the analysis scripts from the Genome Assembly Gold Standard Evaluation (GAGE) work to provide summary statistics about the contig and scaffold sequences resulting from a de novo genome assembly process.

Output

A single output is generated by this tool which is a tabular file containing statistics about the contig and scaffold sequences.

Acknowledgement

We thank the GAGE team for making their evaluation scripts available to the community. The GAGE evaluation is available here. The GAGE work can be cited using the following reference:

GAGE: A critical evaluation of genome assemblies and assembly algorithms
Steven L. Salzberg, Adam M. Phillippy, Aleksey Zimin, Daniela Puiu, Tanja
Magoc, Sergey Koren, Todd J. Treangen, Michael C. Schatz, Arthur L. Delcher,
Michael Roberts, Guillaume Marçais, Mihai Pop, James A. Yorke
Genome Res. 2012 March; 22(3): 557–567. doi: 10.1101/gr.131383.111

This tool was installed from a ToolShed, you may be able to find additional information by following this link: http://gigatoolshed.net/view/peterli/gage_analysis