Benchmarking metacache-gpu

[pojeda]

Hi,

In the manuscript https://arxiv.org/abs/2106.08150, some benchmarks are done for metacache-gpu and Kraken2. I was wondering if it is possible to get the input files and data for metacache-gpu and Kraken2 so that I could perform the benchmark in my local cluster?

/Pedro

[muellan]

The reference genomes from RefSeq can be downloaded either directly at the NCBI or through the script download-ncbi-genomes that comes with MetaCache. However, the script downloads the latest RefSeq release (which is larger) and you might need to manually download all complete bacterial, viral and archaea genomes from RefSeq Release 202 used in the paper from the NCBI. The HiSeq and MiSeq benchmark datasets are from the original Kraken paper and can be found online. The eucaryotic genomes used in the AFS dataset and the Kal_D dataset are from this paper and you should be able to find them in public databases through their accession numbers.

[pojeda]

Hi,

Thanks for your comments. I meant the command lines that you used for Kraken2 and Metacache that led to equivalent simulations.

/Pedro