seqsero2

SeqSero2

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Salmonella serotype prediction from genome sequencing data.

Documentation : https://github.com/denglab/SeqSero2

Citation : https://journals.asm.org/doi/10.1128/aem.01746-19

Directory tree:

seqsero2
├── sample
│   ├── SeqSero_log.txt
│   ├── SeqSero_result.tsv
│   └── SeqSero_result.txt
└── seqsero2_results.txt

Example file for an individual sample (sample/SeqSero_result.tsv)

sample	Output directory	Input files	O antigen prediction	H1 antigen prediction(fliC)	H2 antigen prediction(fljB)	Predicted identification	Predicted antigenic profile	Predicted serotype	Note
salm_GCA_001652385.2	/Volumes/IDGenomics_NAS/Bioinformatics/eriny/testing_grandeur/2024-02-02-02/work/37/b0828917a37fc243a4c41eec4e632c/seqsero2/salm_GCA_001652385.2	salm_GCA_001652385.2.fasta	4	i	1,2	Salmonella enterica subspecies enterica (subspecies I)	4:i:1,2	Typhimurium	

Example file for a run (seqsero2_results.txt)

sample	Output directory	Input files	O antigen prediction	H1 antigen prediction(fliC)	H2 antigen prediction(fljB)	Predicted identification	Predicted antigenic profile	Predicted serotype	Note
salm_GCA_001652385.2	/Volumes/IDGenomics_NAS/Bioinformatics/eriny/testing_grandeur/2024-02-02-02/work/37/b0828917a37fc243a4c41eec4e632c/seqsero2/salm_GCA_001652385.2	salm_GCA_001652385.2.fasta	4	i	1,2	Salmonella enterica subspecies enterica (subspecies I)	4:i:1,2	Typhimurium	
salm_GCA_013344545.1	/Volumes/IDGenomics_NAS/Bioinformatics/eriny/testing_grandeur/2024-02-02-02/work/8f/7ae898a45d4e9c255147c9a6a98323/seqsero2/salm_GCA_013344545.1	salm_GCA_013344545.1.fasta	1,3,19	g,s,t	-	Salmonella enterica subspecies enterica (subspecies I)	1,3,19:g,s,t:-	Senftenberg	
salm_GCA_019710395.3	/Volumes/IDGenomics_NAS/Bioinformatics/eriny/testing_grandeur/2024-02-02-02/work/99/7cf9c5bfbde2ac1d02e8e5e24d4716/seqsero2/salm_GCA_019710395.3	salm_GCA_019710395.3.fasta	4	-	-	Salmonella enterica subspecies enterica (subspecies I)	4:-:-	I 4:-:-	H antigens were not detected. This is an atypical result that should be further investigated. Most Salmonella strains have at least fliC, encoding the Phase 1 H antigen, even if it is not expressed.