optional arguments:¶

-h, --help

show this help message and exit

-i INPUTFILE [INPUTFILE ...], --inputfile INPUTFILE [INPUTFILE ...]

FASTA or FASTQ input files.

-o OUT_PATH, --outputPath OUT_PATH

Path to blast output

-tmp TMP_DIR, --tmp_dir TMP_DIR

Temporary directory for storage of the results from the external software.

-mp METHOD_PATH, --methodPath METHOD_PATH

Path to method to use (kma or blastn)

-p DB_PATH, --databasePath DB_PATH

Path to the databases

-d DATABASES, --databases DATABASES

Databases chosen to search in - if none are specified all are used

-l MIN_COV, --min_cov MIN_COV

Minimum coverage

-t THRESHOLD, --threshold THRESHOLD

Blast threshold for identity

-ao ACQ_OVERLAP, --acq_overlap ACQ_OVERLAP

Genes are allowed to overlap this number of nucleotides. Default: 30.

-matrix, --matrix

Gives the counts all all called bases at each position in each mapped template. Columns are: reference base, A count, C count, G count, T count, N count, - count.

-x, --extended_output

Give extended output with alignment files, template and query hits in fasta and a tab separated file with gene profile results

-q, --quiet