An assembly of reads, contigs and scaffolds

A blog on all things newbler and beyond

Introduction

Posted by lexnederbragt on February 9, 2010

With this blog I intend to share some of my experiences with the newbler assembly program from 454, also known as gsAssembler, or gsMapper. It is the software suite developed by 454 Life Sciences to be used with the sequence data coming from the GS FLX sequencing instrument.

Reads: those are the fragments, small bits and pieces that I write about in the blog.

Contigs: together, these fragments make a larger pieces of information on the subject.

Scaffolds: by building bridges between the subjects I hope to reach a complete overview of the newbler program. Granted, there will be gaps, as there are also gaps in my knowledge, but in the end, the information should be useful guide to newbler.

I learned a lot about newbler when working with data from bacterial genome assemblies, and the cod genome project, for which I am one of the bioinformaticists. I am also connected to the 454 node of the Norwegian High-Throughput Sequencing Centre (NSC), where many of our users are relying on newbler for their projects.

The first post will describe step-by-step how newbler generates contigs and scaffold from reads. So, let’s start the assembly!

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