How To Visualise Newbler Output?

Question

[Biomonika (Noolean)]

Hi all,

I am assembling 454 reads with newbler. It is installed on distant computer, so I can use just text mode. The assembly is done, but I dont know how to visualise the results - I would like to see all mapped reads. What programs should I use for visualisation? Or how to export alignment in text mode in format, that can other programs use?

Any advice will be appreciated.

Answer 1

[Leonor Palmeira]

According to the version of newbler you are using:

newbler --version

I would search for the appropriate version of the software manual (here is version 2.3). You can also request Roche for a new version of the software and the manual is included in the package. You will see that some of the output files contain information on the mapped and unmapped reads, on the coverage, ... The .ace final file will contain all the assembly information, and this can be viewed with HawkEye or EagleView, for instance.

[Biomonika (Noolean)]

Thank you for advice that .ace contains alignment information. I have opened this in Geneious and it worked perfectly for me, thats why I ticked you as an answer. Thanks everyone for suggestions and advice!

Answer 2

[Gmoney]

As of Newbler 2.6, they support .bam output. I don't have the command line flag off hand, but it is a tick on gsMapper's output.

After your run, you'll end up with 454Contigs.bam. This file can be manipulated by all kinds of command line tools.

For visualization, I use IGV from Broad Institute on my local machine.. Comes with most of what you'll want out of the box. Supports extra tracks, and is all around whizbang. For other stats, I use a combination of bedtools/samtools and R. I primarily do exon capture, so its very region of interest.

[Leonor Palmeira]

Last time I used it, the Roche software didn't provide a .bam output, but it did provide .ace output. Either way, it wouldn't be a tick in gsMapper here (no graphical interface available) but an option in newbler (don't remember which by heart).

[Gmoney]

I use runMapping (command line toy via Roche) to do my command line mapping. The flag is -bam strangely enough for .bam output.

Oh, the other reason I dig .bam rather than ace is its ease of use with all the samtools/bedtools toys.

Answer 3

[Fwip]

If you can't get a graphical display at all (no X-forwarding, no ability to download the files for local viewing, etc), one option is to use "samtools tview." It's really not a nice way to look at the data, but it's a possible fallback option if you can't use a better solution.