Running

meningotype

In silico typing of Neisseria meningitidis contigs

• Serotyping
• MLST
• Finetyping (porA, fetA, porB)
• Bexsero antigen sequence typing (BAST) (fHbp, NHBA, NadA, PorA)

However, for MDU use only Serotyping and finetyping are relevant.

MDU use

When running meningotype for MDU use a positive control must be included 9997-11111

# include all genotypes
$ meningotype --all NMA.fasta > out.tab

SAMPLE_ID  SEROGROUP  ctrA    MLST    PorA       FetA    PorB            fHbp    NHBA    NadA    BAST
NMA.fasta  A          ctrA    4       7,13-1     F1-5    NEIS2020_28     5       29      0       639

# type lots of files at once
$ meningotype --all *.fna > out.tab

SAMPLE_ID  SEROGROUP  ctrA    MLST    PorA       FetA    PorB            fHbp    NHBA    NadA    BAST
A.fna      A          ctrA    4       7,13-1     F1-5    NEIS2020_28     5       29      0       639
B.fna      B          ctrA    8       5-2,10-1   F3-6    NEIS2020_12     16      20      8       150
C.fna      C          ctrA    177     21,26-2    F1-5    NEIS2020_3      17      101     9       118
W.fna      W          ctrA    11      5,2        F1-1    NEIS2020_244    623     29      6       141
X.fna      X          ctrA    181     5-1,10-1   F4-23   NEIS2020_509    391     358     0       -
Y.fna      Y          ctrA    23      5-2,10-1   F4-1    NEIS2020_67     25      7       0       228

Output can be passed to the following command to generate LIMS ready output

sed 's/\/contigs\.fa//g' out.tab | python3 /home/agoncalves/dev/qc_tools/mdu-lims-filter.py --tool meningotype "RUN_ID_meningotype" -