- python 3.10.4
- blast 2.10.1
- click 8.1.3
- kma 1.3.23
python Monotyper/main.py --pcr_products --threads 8 --paired_fastq R1.fastq.gz R2.fastq.gz
-h, --help Show this message and exit.
--min_id FLOAT Minimum percent identity to accept a match. [0-100]
--min_cov FLOAT Minimum coverage of the gene to accept a match.
[0-100]
--paired_fastq TEXT... Paired-end reads input, list both read files
separated by a space. Can be in .fastq or .fastq.gz
format. e.g. '--paired_fastq R1.fastq.gz
R2.fastq.gz'
--single_fastq TEXT Single-end reads input. Can be in .fastq or
.fastq.gz format. e.g. '--single_fastq R.fastq.gz'
--fasta TEXT Fasta input. e.g. '--fasta assembly.fa'
--batch_input TEXT Path to text file containing list of input file
paths to serotype. The format for each line should
be as follows, separated by tabs: [input type
(fasta, single_fastq, or paired_fastq)] [path to
file] [path to other paired read file if
necessary]. Lines starting with '#' will be ignored
--blast_only Only run blast, default is to run fasta files with
kma and blast
--pcr_products Use database built from theoretical pcr products
rather than entire genes
--gapped_blast Use gapped blast instead of ungapped. This more
closely matches the kma matching results
--remake_dbs Remake the databases at start of run
--kma_only Only run kma, default is to run fasta files with
kma and blast
--csv Set output type to .csv, default is .tsv
--threads INTEGER Number of threads to use, default is 1
--min_depth TEXT Minimum read depth for gene to be called
--allele_frequency TEXT Minimum allele frequency for calling SNPs, default
is 0.9