seqsero1
Salmonella serotyping from genome sequencing data
Usage
seqsero -m
<data_type>
-i
<input_data>
[-b
<BWA_algorithm>]
Options
-
-h, --help -
show this help message and exit
-
-m {1,2,3,4} -
<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly)
-iI [I ...]-
<string>: path/to/input_data
-
-b {sam,mem} -
<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam