Running Mercat2

Dependencies

MerCat2 runs on python version 3.9 and higher.

MerCat2 can run without external dependencies based on the options used.

Required dependencies:

When a raw read .fastq file is given
- Fastqc
- Fastp
For bacteria/archaea rich samples (-prod option)
- Prodigal
For eukaryote rich samples or general applications (-fgs option)
- FragGeneScanRs
Use this script for FragGeneScanRS

conda install -c bioconda fastqc fastp prodigal

Note

These are available through BioConda, except FragGeneScanRS, which is included in the MerCat2 distribution.

MerCat2 uses a substantial amount of memory when the k-mer is high
Running MerCat2 on a personal computer using a k-mer length of ~4 should be OK
Total memory usage can be reduced using the Chunker feature (-s option), but keep in mind that in testing when the chunk size is too small (1MB) some of the least significant k-mers will get lost.
This does not seem to affect the overall results, but it is something to keep in mind. Using the chunker and reducing the number of CPUs available (-noption) can help reduce memory requirements.

Note

The speed of MerCat2 can be increased when more memory or computer nodes are available on a cluster and using a chunk size of about 100Mb.