fastKaptive is a Blast-based R written software to search and extract capsule synthesis loci in bacterial genomes. It has been used and tested on genomes of the Enterobacteriales, as described in [1]. The code was designed to extract to locus regions, based on a model of Escherichia coli [2]:
- cps locus region, associated with the synthesis of O-antigens in E. coli,
- kps locus region, associated with the synthesis of K-antigens in E. coli.
The approach is based on a previously published and tested method, Kaptive [3], but has been reoptimised for scanning large sets of genomes by avoiding tblastx and using blastn instead.
The software uses blastn and gzip as dependencies, and it order to work they should be installed prior to using fastKaptive and the commands should be visible in PATH. Also, these R packages need to be installed beforehand via the install.packages() command:
seqinrigraphoptparse
The code was developed on Mac OS X and should work on Linux-based platforms via a command line. The programme should be launched from a working directory by revoking:
Rscript --vanilla ${fK_PATH}/main.R (options)
where fK_PATH is the location of the fastKaptive directory.
Using the -h option, one can display the options:
Options:
-l LOCUS.NAME, --locus.name=LOCUS.NAME
Which locus to search: cps [default] or kps
-e, --extended.db
Use an extended locus search database [default FALSE]
-D, --distant.search
Search in distant bacteria using blastn instead of megablast [default FALSE]
-p PATH.FILE, --path.file=PATH.FILE
File with path names to all assemblies [default paths.input.txt]
-o OUTPUT.FOLDER, --output.folder=OUTPUT.FOLDER
Name of the output folder [default extract.output]
-h, --help
Show this help message and exit
The first option -l specifies the locus which should be searched, either cps or kps. Any other option will return an error.
The second option -e specifies whether an extended database should be used. By default the code uses a high-quality locus references from Klebsiella, Escherichia/Shigella and Salmonella for cps and only Escherichia for kps. However, an extended reference database, obtained by searching 27,365 genomes of Enterobacteriales in [1], and extracting good quality loci from draft genomes, amounting to 994 references for cps and 106 references for kps.
The third option -D specifies whether blastn option should be used with blast instead of megablast: if used, a more time-consuming search will ensue, resulting in more accurate searches in other species of Enterobacteriales. It is recommended to use when searching outside of the Enterobacteriaceae family.
The fourth option -p specifies the location of a file with assembly paths. If these paths are incorrect, the code will return an error. This is a mandatory option.
The fifth option -o specifies the name of the output folder.
- Holt KE, Lassalle F, Wyres KL, Wick R & Mostowy RJ, Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales, submitted
- Whitfield C Biosynthesis and assembly of capsular polysaccharides in Escherichia coli, Annu Rev Biochem. 2006;75(1):39-68. doi:10.1146/annurev.biochem.75.103004.142545.
- Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR & Holt KE, Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial Genomics. 2016;2(12):e000102. doi:10.1099/mgen.0.000102.