An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Posts Tagged ‘454ScaffoldContigs.fna’

Newbler output V: the 454ContigScaffolds.txt and 454ScaffoldContigs.fna

Posted by lexnederbragt on July 12, 2011

Filling the gaps (picture from http://www.ifaonline.co.uk)

In the post on what is new in newbler version 2.6, I introduced the -scaffold option. Briefly, with this option instances (i.e. the consensus sequence) of repeats are placed in gaps. As I mentioned, setting -scaffold results in two extra files. With this post, I will explain these in detail.

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Posted in How it works, Newbler output | Tagged: , , , , , , | 1 Comment »