Options for using mercat2

Usage

These are the different options that can be used with mercat2.py

usage: mercat2.py [-h] [-i I [I ...]] [-f F] -k K [-n N] [-c C] [-prod] [-fgs] [-s S] [-o O] [-replace] [-lowmem LOWMEM] [-skipclean] [-toupper] [-pca] [--version]

Example: mercat2.py -h

Options:	Description
-h, --help	Shows this help message and exit
-i I [I ...]	Path to input file(s)
-f F	Path to folder containing input files
-k K	kmer length
-n N	No of cores [auto detect]
-c C	Minimum kmer count [10]
-prod	Run Prodigal on fasta files
-fgs	Run FragGeneScanRS on fasta files
-s S	Split into x MB files. [100]
-o O	Output folder, default = 'mercat_results' in current directory
-replace	Replace existing output directory [False]
-lowmem LOWMEM	Flag to use incremental PCA when low memory is available. [auto]
-skipclean	Skip trimming of fastq files
-toupper	Convert all input sequences to uppercase
-pca	Create interactive PCA plot of the samples (minimum of 4 fasta files required)
--version, -v	Show the version number and exit

Mercat2 assumes the input file format based on the extension provided

• Raw fastq file: ['.fastq', '.fq']

• Nucleotide fasta: ['.fa', '.fna', '.ffn', '.fasta']

• Amino acid fasta: ['.faa']

• It also accepts gzipped versions of these filetypes with the added '.gz' suffix

Usage examples

These are different ways MerCat2 can be implemented, running on samples based the following

Type	Script
Protein file (protein fasta - '.faa')	mercat2.py -i file-name.faa -k 3 -c 10
Nucleotide file (nucleotide fasta - '.fa', '.fna', '.ffn', '.fasta')	mercat2.py -i file-name.fna -k 3 -n 8 -c 10
Nucleotide file raw data (nucleotide fastq - '.fastq')	mercat2.py -i file-name.fastq -k 3 -n 8 -c 10
Many samples within a folder	mercat2.py -f /path/to/input-folder -k 3 -n 8 -c 10
Sample with prodigal option (raw reads or nucleotide contigs - '.fa', '.fna', '.ffn', '.fasta', '.fastq')	mercat2.py -i /path/to/input-file -k 3 -n 8 -c 10 -prod
Sample with FragGeneScanRS option (raw reads or nucleotide contigs - '.fa', '.fna', '.ffn', '.fasta', '.fastq')	mercat2.py -i /path/to/input-file -k 3 -n 8 -c 10 -fgs

Note

The prodigal and FragGeneScanRS options run the k-mer counter on both contigs and produced amino acids

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