Newbler is no longer available..

[shannonmargaret]

One of the dependencies of the MeGAMerge program, Newbler, is no longer available as Roche has shut down it's sequencing division. Is there a way to get around this dependency and still use MeGAMerge? Thanks! Shannon

[scholzmb]

Thanks for the heads up. Exploring options now. I don't want to distribute their tool w/o permission, and I don't know if we have a module to do small contig merging without newbler.

Long term goal (will open a new issue) would be to create different modules for the short contig assembly, and allow mix and match.

[pdalcinmartins]

I am also stuck at this point. Any updates on this? Thanks! -Paula

[shannonmargaret]

Hi Paula, Thanks for checking in - I've told several people about your method and it is really a shame that it isn't currently useable. I have moved on to other projects, and used a basic meta genome assembler instead. I hope that you find a resolution to this issue. Please keep me posted on your progress. Best, Shannon

On Mon, Sep 25, 2017 at 10:58 AM, pdalcinmartins notifications@github.com wrote:

I am also stuck at this point. Any updates on this? Thanks! -Paula

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-- Shannon Soucy, PhD Zhaxybayeva Lab Dartmouth College

[pdalcinmartins]

Thanks, Shannon. What have you used instead?

[shannonmargaret]

I like to use a couple of different assemblers, I've found Spades(Khmer based) and IDBA (be bruin based) to perform the best, and then I run FastQC on the assembled datasets to get an idea of which platform worked better, and how much better it was. Simultaneously I run the raw data through a taxonomy assignment program like Kaiju or Megan, and then pull the reads from the taxa I'm interested. After that I map the reads assigned to a single taxon back to the assembled data using Bowtie and make sure that reads from the same taxa are mapped to the same assembled contig.

Hopefully this makes sense. Best, Shannon

On Mon, Sep 25, 2017 at 11:13 AM, pdalcinmartins notifications@github.com wrote:

Thanks, Shannon. What have you used instead?

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-- Shannon Soucy, PhD Zhaxybayeva Lab Dartmouth College

[pdalcinmartins]

Thanks, Shannon! Well, my case is a little different - I already have the assemblies (and no time for reassembly, unfortunately) and really need something to merge them. Your tool would have been awesome. Still, I will see if Roche replies or somebody I know has Newbler. -Paula

[scholzmb]

Paula,

One other option, which is probably not ideal, but gives you something to work with:

The newbler portion of the code is to run assembly on many small contigs, to reduce the runtime of Minimus2. If your assemblies are reasonably good (e.g. not tens of thousands of small contigs, say less than 2 KB), we can probably find a way to just SKIP the newbler portion entirely.

I haven’t really found another assembler that works as quickly as newbler to run assembly on small contigs, sadly.

Thoughts?

From: pdalcinmartins [mailto:notifications@github.com] Sent: Monday, September 25, 2017 10:25 AM To: LANL-Bioinformatics/MeGAMerge MeGAMerge@noreply.github.com Cc: Scholz, Matthew B matthew.b.scholz@vanderbilt.edu; Comment comment@noreply.github.com Subject: Re: [LANL-Bioinformatics/MeGAMerge] Newbler is no longer available.. (#6)

Thanks, Shannon! Well, my case is a little different - I already have the assemblies (and no time for reassembly, unfortunately) and really need something to merge them. Your tool would have been awesome. Still, I will see if Roche replies or somebody I know has Newbler. -Paula

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