Start from assemblies

[susheelbhanu]

Hi,

Is it possible to start the run directly from assemblies?

If yes, could you point me to the direction?

Thanks,
Susheel

[SteamedFish6]

Hi Susheel,

MetaRanker quantifies genes when ranking ARG risk of metagenomic samples, so reads are needed.

Assemblies are generated from reads, so please just take reads as MetaRanker's input as well.

In the future we prepare to develop a genome-ranking mode, then you can start the run directly from assemblies.

Thanks for your advice.
SteamedFish6

[susheelbhanu]

May be easier to run using BAM files in that case instead of reads. Something to consider when you develop that next iteration.

Is there a timeline?

[SteamedFish6]

Hi Susheel,

MetaRanker uses local database, and it generates corresponding BAM files during middle process -- Although it's not efficient when integrating MetaRanker with other pipelines.

For genome-ranking mode, annotation with BLAST may help, but how to rank the risk still needs to consider. Binning approach is also important. Further investigation will be made this year.