Using Metabat output in JGI ELVIZ

[Former user]

Hi, I was wondering if we can use the output from Metabat in someway to be able to visualize in JGI's ELVIZ. We are trying to assemble single cell sequencing data and hence coverage might be tricky. We were trying to look more at compositional features like tetra nucleotide frequency or GC content.

Thanks! Snehal

[Don Kang]

If GC is used, you can use Elviz right away. But for TNF, you need distance matrix and subsequently low dimensional projection so that you can have 2d coordinates that you can use it on Elviz. However, currently it is not straightforward to extract TNF distance out of MetaBat. One work-around way is to extract TNF signature using other tools and calculate Euclidean distance.