OMAP-KP

OMAP-KP is an R script that performs ordered mapping and assignment for plasmid identification in NGS data from KP.

Dependencies

• To run OMAP-KP: BLAST [>= 2.13] R [>= 3.6.1] data.table [>=1.13] IRanges [>=2.36]

Usage

Prepare your Input

1. BLAST reference The plasmids.repr.fas from KleTy can be found at https://github.com/zheminzhou/KleTy
   The mobileOG-db_beatrix-1.6.faa can be found at https://mobileogdb.flsi.cloud.vt.edu/entries/database_download

   makeblastdb -in  ./dir/to/ref/plasmids.repr.fas  -dbtype nucl  -parse_seqids -out ./dir/to/ref/plasmids.repr.fas

   makeblastdb -in ./dir/to/ref/mobileog_target.faa -dbtype prot  -parse_seqids -out ./dir/to/ref/mobileog_target

2. Cluster and MGE annotation file Available here in the repository ("./KleTy/plasmids.repr.clu" and "./mobileOG-db/mge_target.txt")

Run OMAP-KP

1. To run the script:

   Rscript OMAP_v2.R  ./dir/to/your/input_genome.fasta  ./dir/to/your/output.dir/  ./KleTy/plasmids.repr.fas ./mobileOG-db/mobileog_target ./KleTy/plasmids.repr.clu  ./mobileOG-db/mge_target.txt

Output

1. [filename]_pls.tsv A file contains: filename, pls_id, cluster, scovs, and slen.
2. [filename]_raw.tsv A file contains the raw data of hc_dt.tsv file, including the names of contigs assigned to the plasmid.

Supplementary files

The validation dataset suggested a recall rate of 85.27% for plasmids exceeding 10,000 bp in 56 draft genomes. (Updated in 2025/01/17)
https://github.com/HHeng-bioinfo/OMAP-KP_seq