An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Posts Tagged ‘read depth’

Newbler output III: the 454ContigGraph.txt file

Posted by lexnederbragt on April 13, 2010

The single file I’ll discuss today has in fact almost the entire assembly in it, besides the actual sequences (although even some of these are also included, see below). As explained in my first post, newbler (as many other assembly programs) builds a contig graph. Contigs are the nodes, and reads spanning between them (starting in one contig and continuing or ending in another) indicate the edges. All the information on this graph, except the actual read alignments and consensus contigs, is in the 454ContigGraph.txt file.

The file is divided into several sections, for each one the lines start with a capital letter, except for the first section.

Putting together an assembly...

Section 1) Contig statistics

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