is there publicly available tool for assembly of bionano data

Question

[eebloom]

I have raw bionano data (.bnx.gz). I want to assemble this data to generate contigs (.cmap). I dont have access to a bionano machine and so it seems I cant use the bionano solve software easily. Is there a good open access OM assembly tool I can use?

[GenoMax]

If you are working with a bionano service provider, it is generally most efficient to have them do some of the initial analysis. If you acquired this data from a public source then perhaps OMTools option mentioned below may work.

[eebloom]

thanks, I think we did have some variant analysis done on it a while back but not any assembly. I'm digging up some older data so probably need to do the analysis myself

Answer 1

[Aleksandra]

The academic standard is OMTools for de novo assembly of .bnx files. It includes OMBlast for molecule alignment and generates .cmap consensus maps. However, the primary value of Bionano data is in hybrid scaffolding. I recommend using OMTools to scaffold a long-read (PacBio/ONT) sequence assembly for a chromosome-level result.

[GenoMax]

When recommending software packages, it is helpful to provide links to them. There can be packages with similar names leading to confusion.

That said, are you sure OMTools is still a valid option. It looks like the last release was 5 years ago and there have been changes to bionano offerings in that time, specially if the data original poster has is new.

[eebloom]

thankfully it IS old data :) but a more recent tool would be ideal

[Aleksandra]

My recommendation regarding OMTools was based specifically on comment about working with older data, as it was a stable academic standard for obsolete .bnx formats. For any future projects, I would still strongly advise looking into TULIP as a more modern and user-friendly solution. Once again, I apologise for my previous response.

[GenoMax]

No need to apologize. You are trying to help people, which is great. My comment was mainly to improve your post.

In comment above you mentioned TULIP which I assume is a software package without providing a link. Only thing I seem to find is https://github.com/Generade-nl/TULIP Was this the package you had in mind, if not, can you provide a link.

[Aleksandra]

Unfortunately, no, this link is not to the tool I was talking about, but I think the only thing I can confidently recommend is the official command-line tools from Bionano Genomics itself. For example, Bionano Solve and Bionano Tools script set. It takes your assembly from sequencing data (e.g., contigs from PacBio/ONT/Illumina) and uses Bionano optical maps. https://bionano.com/software-downloads/

[eebloom]

Can I use this bionano software on any linux machine / hpc cluster? Im struggling with the documentation and it seems I need some sort of token / access key.

[eebloom]

I cant see a command on OMToolsManual.pdf which says it takes .bnx.gz files and assembles them in to contigs (.cmap)

[Aleksandra]

There is no single assemble command in OMTools. It is not a monolithic program, but a set of separate scripts that must be executed sequentially. First, you need to perform an ‘all-vs-all’ alignment of .bnx molecules using OMBlast to obtain overlap data. Then you use a series of scripts (mostly in Perl, often found in the misc/ directory) to process the OMBlast output. The key script that starts the process is omchain.pl. It is followed by others for constructing the graph and resolving it.