Scaffolding and assembly quality evaluation/visualisation tools?

[MikhailFokin]

Hi All,

I am working with de-novo seq of fungal genomes. Sometimes I am really frustrating with different assemblies/scaffolding structures I am able to get from the same datasets just varying assembly parameters. It is especially important for large clusters of genes (up to 100-200kb), where I have to be very confident with order/orientation of genes.

What I am looking for: the software to verify (probably just visually) the quality of linking contigs into scaffolds, based on paired/mate reads mapping and quality info.

The options I've found now are:
- Tablet
- Hawkeye and AMOS

Are there somebody using these? Any other suggestions?
Thank you

[boetsie]

The tool 'Bandage' can visualize assemblies from SPAdes using the fastG format it produces. You can load the results of the final scaffolds or the intermediate K-mer contigs. Also, you can BLAST sequences (e.g. gene sequences) to see where it sits within the assembly graph.

The tool is available here;

http://rrwick.github.io/Bandage/

Boetsie

[bastianwur]

You can try some of the tools which evaluate the quality of the mapping like CGAL or RSEM-EVAL. Maybe these can give you an idea which assembly is better.