Question: software for constructing contigs and scaffold
0
gravatar for njs531
4.8 years ago by
njs53120
United Kingdom
njs53120 wrote:

Hi,

I don't have any experience in assembling bacterial genome before. I have analyzed some Nextgen sequencing data before but I was looking at the gene expression. At the moment, I'm working on assembling bacterial genome from ion torrent reads. I have assembled my reads using Newbler (gsAssembly) . What I'm supposed to do next is to try to put the contigs and scaffold together in order to view how the genome is positioned/orientated across chromosomal and plasmids and also to determine how many plasmids are present in the species. My supervisor suggested me to do this manually (as in check the alignment by eye) . Is there any software that can perform contigs/scaffold construction without a reference genome ? Ive read about contiguator and scaffolder but they require reference genome.

bacterial contigs assembly • 3.5k views
ADD COMMENTlink modified 4.8 years ago by Adrian Pelin2.2k • written 4.8 years ago by njs53120
2

Please have a look, hope you will find your answer: 

http://omictools.com/scaffolding/

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by HG1.1k
2
gravatar for Adrian Pelin
4.8 years ago by
Adrian Pelin2.2k
Canada
Adrian Pelin2.2k wrote:

What you are looking for is a De Novo Assembler. These tools take you from NGS reads to contigs & scaffolds.

There are a few out there, MIRA, Newbler, SOAPdenovo, Velvet, Spades

Here is a big list: http://en.wikipedia.org/wiki/Sequence_assembly

ADD COMMENTlink written 4.8 years ago by Adrian Pelin2.2k
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