update to v1.3.1

• Converted the sequences of some alleles to their reverse complement sequences in the SeqSero2 database.
• Deleted some alleles from the SeqSero2 database because of the existence of mutations.
• Added a fliC 1,5,7 allele and a fliC 1,2,7 allele into the SeqSero2 database.
• Deleted the O54 allele.
• Fixed the bug that caused the misidentification of O9 and O2 by the micro-assembly workflow.
• Used Spades v3.15.5 to prevent the bug when running the micro-assembly workflow in Mac with M2 chip.

update to v1.2.1

• Use a unified nanopore workflow (-t 5) to replace the separate workflows for nanopore data in FASTA and FASTQ format.
• Change "Predicted subspecies" to "Predicted identification" in output file.
• Use full name of Salmonella species/subspecies for "Predicted identification" in output file.
• Report “Salmonella enterica” when subspecies identification of a Salmonella enterica genome cannot be definitively determined.
• Subspecies VII by SalmID will be reported as subspecies IV.
• Modify note for inconsistency of subspecies identification between KWS and SalmID.
• Modify notes for special determinants.
• Two likely mis-annotated H antigen alleles (AY353514 and AY353272) were removed from allele database.

update to v1.1.1

• Fixed a problem with the setting of an output path using -d option

update to v1.1.0

• Fixed misidentification of O-9,46 as O-9 for certain O-9,46 serotypes (e.g. Ouakam)
• Fixed misidentification of O-9 as O-9,46 by the k-mer workflow
• Fixed misidentification of O-2 as O-9 for certain O-2 serotypes (e.g. Paratyphi A)
• Fixed misidentification of O-4 as O-9,46,27 by the micro-assembly workflow
• Fixed misidentification of fliC-b as fliC-l,v by the k-mer workflow when fljB-l,w was present in the query genome
• Fixed misidentification of fliC-z as fliC-l,z13,z28 by the k-mer workflow when fljB-l,z13,z28 was present in the query genome
• Fixed misidentification of Okatie as 13:g,t:-
• Fixed misidentification of Fulica as 4: a:-
• Modified interpretation of no antigen calls (“-”)
• Increased SalmID threshold for subspecies identification
• Fixed unexpected subspecies designation in output for serotypes that do not have a “serotype name”
• New -n option to allow sample name designation
• Fixed premature exit from the micro-assembly workflow without proper output when non-Salmonella genomes are queried
• New tab-delimited text output “SeqSero_result.tsv”, new -s option to suppress header in the output
• Changed path to allele database to prevent write permission issue

v1.0.2

Fixed the bug that caused the misidentification between O1,3,19 and O3,10
Noted in output when a predicted serotype does not exist in the K-W scheme
Added conda installation

v1.0.0

version 1.0.0

v0.1

Alpha-test version of SeqSero2. The official version will be released soon.