QUAST
What it does
QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.
If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.bioinf.spbau.ru/manual.html>`_.
Using Quast without reference
Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:
- Quast report in HTML format
- `Contig viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file)
- `Quast report <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_ in Tab-delimited format
- Quast log (a file technical information about Quast tool execution)
The tab delimited Quast report will contain the following information::
Assembly pit_fna cef_fna car_fna # contigs (>= 0 bp) 100 91 94 # contigs (>= 1000 bp) 62 58 61 Total length (>= 0 bp) 6480635 6481216 6480271 Total length (>= 1000 bp) 6466917 6468946 6467103 # contigs 71 66 70 Largest contig 848753 848766 662053
