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Old 02-01-2018, 05:27 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076
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Welcome to SA!

You can use FastQC for assessment of quality of initial read data. This is pretty much the de facto program people use. The lab that made FastQC has many informative blog posts about data quality/observations at their QC Fail site.

Quast is what you would want to use for assessment of assemblies.

If these are bacterial genomes then Mauve allows you to do genome-wide alignments to quickly identify rearrangements.\

I recommend BBMap suite (multiple threads here on various tools included). This suite has many tools that allow you to work with NGS data.
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