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Spades E coli assembly visualised with bandage

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posted on 30.10.2015 by Lex Nederbragt

While preparing for a course on de novo genome assembly, I tried out the excellent Bandage program for viewing assembly graphs. One spades assembly stuck out, as it showed a 'knot' of short contigs. Inspection of the sequencing of these contigs showed them to be derived from the rRNA loci of the genome (rRNA and tRNA genes). After I posted an image of the graph on twitter, a fellow researcher asked me for a citable copy of the figure. This figshare entry is meant to provide just that.

 

I've also included the fastg file so those interested can load it into bandage.

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