Difference between revisions of "Assembly-stats"
(Created page with "= Introductions = Some assembly programs do not output any summary details regarding the assembly they produce. This program is useful in listing out various ket quality (or...") |
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Some assembly programs do not output any summary details regarding the assembly they produce. This program is useful in listing out various ket quality (or perhaps better said, completeness) statistics on the assembly. It is developed by the Sanger Pathogens team and is not particulary complicated having quite simple outputs, which are nonetheless very useful. | Some assembly programs do not output any summary details regarding the assembly they produce. This program is useful in listing out various ket quality (or perhaps better said, completeness) statistics on the assembly. It is developed by the Sanger Pathogens team and is not particulary complicated having quite simple outputs, which are nonetheless very useful. | ||
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| + | = Usage = | ||
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| + | Quite simple, though you need to load the module first: | ||
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| + | module load assembly-stats | ||
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| + | And then | ||
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| + | assembly-stats scaffolds.fasta | ||
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| + | If <tt>scaffolds.fasta</tt> is your assembly file, which it probably will be, if you used SPAdes for your assembly. And as SPAdes does not summarise its assembly, this program is a good way to go. | ||
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= Links = | = Links = | ||
Homepage is [https://github.com/sanger-pathogens/assembly-stats here]. | Homepage is [https://github.com/sanger-pathogens/assembly-stats here]. | ||
Latest revision as of 17:49, 10 February 2017
Introductions
Some assembly programs do not output any summary details regarding the assembly they produce. This program is useful in listing out various ket quality (or perhaps better said, completeness) statistics on the assembly. It is developed by the Sanger Pathogens team and is not particulary complicated having quite simple outputs, which are nonetheless very useful.
Usage
Quite simple, though you need to load the module first:
module load assembly-stats
And then
assembly-stats scaffolds.fasta
If scaffolds.fasta is your assembly file, which it probably will be, if you used SPAdes for your assembly. And as SPAdes does not summarise its assembly, this program is a good way to go.
Links
Homepage is here.
