In silico typing of Neisseria meningitidis contigs
- Serotyping
- MLST
- Finetyping (porA, fetA, porB)
- Bexsero antigen sequence typing (BAST) (fHbp, NHBA, NadA, PorA)
# install
$ pip install git+https://github.com/MDU-PHL/meningotype.git
# just serotype
$ meningotype NMA.fasta
SAMPLE_ID SEROGROUP ctrA MLST PorA FetA PorB fHbp NHBA NadA BAST
NMA.fasta A ctrA - - - - - - - -
# include all genotypes
$ meningotype --all NMA.fasta
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
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
The simplest way to install dependencies is to use the Brew (MacOS) or Linuxbrew (Linux) packaging system.
$ brew tap brewsci/bio
$ brew install ispcr blast mlst
The easiest way of installing meningotype is using pip:
$ pip install --user git+https://github.com/MDU-PHL/meningotype.git
The --user option will install the package locally, rather than in the global python directory.
Thus, by default, this will install the package in $HOME/.local/, and the executable in $HOME/.local/bin/.
To install the executable in a custom location (e.g., $HOME/bin), use the following:
$ pip install --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/MDU-PHL/meningotype.git
To upgrade to a newer version:
$ pip install --upgrade --install-option="--install-scripts=$HOME/bin" --user git+https://github.com/MDU-PHL/meningotype.git
Once installed, you can run the following to ensure meningotype is successfully working:
$ meningotype.py --test
If everything works, you will see the following:
$ meningotype.py --test
Running meningotype.py on test examples ...
$ meningotype.py A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID SEROGROUP ctrA MLST PorA FetA PorB fHbp NHBA NadA BAST
meningotype/test/A.fna A ctrA - - - - - - - -
meningotype/test/B.fna B ctrA - - - - - - - -
meningotype/test/C.fna C ctrA - - - - - - - -
meningotype/test/W.fna W ctrA - - - - - - - -
meningotype/test/X.fna X ctrA - - - - - - - -
meningotype/test/Y.fna Y ctrA - - - - - - - -
or to check finetyping:
$ meningotype.py --test --finetype
Running meningotype.py on test examples ...
$ meningotype.py A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID SEROGROUP ctrA MLST PorA FetA PorB fHbp NHBA NadA BAST
meningotype/test/A.fna A ctrA - 7,13-1 F1-5 - - - - -
meningotype/test/B.fna B ctrA - 5-2,10-1 F3-6 - - - - -
meningotype/test/C.fna C ctrA - 21,26-2 F1-5 - - - - -
meningotype/test/W.fna W ctrA - 5,2 F1-1 - - - - -
meningotype/test/X.fna X ctrA - 5-1,10-1 F4-23 - - - - -
meningotype/test/Y.fna Y ctrA - 5-2,10-1 F4-1 - - - - -
or to check finetyping and Bexsero antigen sequence typing:
$ meningotype.py --test --all
Running meningotype.py on test examples ...
$ meningotype.py A.fna B.fna C.fna W.fna X.fna Y.fna
SAMPLE_ID SEROGROUP ctrA MLST PorA FetA PorB fHbp NHBA NadA BAST
meningotype/test/A.fna A ctrA 4 7,13-1 F1-5 NEIS2020_28 5 29 0 639
meningotype/test/B.fna B ctrA 8 5-2,10-1 F3-6 NEIS2020_12 16 20 8 150
meningotype/test/C.fna C ctrA 177 21,26-2 F1-5 NEIS2020_3 17 101 9 118
meningotype/test/W.fna W ctrA 11 5,2 F1-1 NEIS2020_244 623 29 6 141
meningotype/test/X.fna X ctrA 181 5-1,10-1 F4-23 NEIS2020_509 391 358 0 -
meningotype/test/Y.fna Y ctrA 23 5-2,10-1 F4-1 NEIS2020_67 25 7 0 228
$ meningotype.py -h
usage:
meningotype.py [OPTIONS] <fasta1> <fasta2> <fasta3> ... <fastaN>
In silico typing for Neisseria meningitidis
Default: Serotyping, MLST and ctrA PCR
PCR Serotyping Ref: Mothershed et al, J Clin Microbiol 2004; 42(1): 320-328
PorA and FetA typing Ref: Jolley et al, FEMS Microbiol Rev 2007; 31: 89-96
Bexsero antigen sequence typing (BAST) Ref: Brehony et al, Vaccine 2016; 34(39): 4690-4697
See also http://www.neisseria.org/nm/typing/
positional arguments:
FASTA input FASTA files eg. fasta1, fasta2, fasta3 ... fastaN
optional arguments:
-h, --help show this help message and exit
--finetype perform porA and fetA fine typing (default=off)
--porB perform porB sequence typing (NEIS2020) (default=off)
--bast perform Bexsero antigen sequence typing (BAST) (default=off)
--mlst perform MLST (default=off)
--all perform MLST, porA, fetA, porB, BAST typing (default=off)
--db DB specify custom directory containing allele databases for porA/fetA typing
directory must contain database files: "FetA_VR.fas", "PorA_VR1.fas", "PorA_VR2.fas"
for Bexsero typing: "fHbp_peptide.fas", "NHBA_peptide.fas", "NadA_peptide.fas", "BASTalleles.txt"
--printseq save porA/fetA or BAST allele sequences to file (default=off)
--updatedb update allele database from <pubmlst.org>
--test run test example
--version show program's version number and exit
To perform in silico serotyping on FASTA files:
$ meningotype <fasta1> <fasta2> <fasta3> ... <fastaN>`
The serotypes are printed in tab-separated format to stdout.
To save results to a tab-separated text file, redirect stdout:
$ meningotype <fasta1> <fasta2> <fasta3> ... <fastaN> > results.txt
To perform in silico serotyping AND finetyping of the porA and fetA genes:
$ meningotype --finetype <fasta1> <fasta2> <fasta3> ... <fastaN>
To save finetyping sequences of the alleles to a file (eg. for uploading "new" sequences to http://pubmlst.org/neisseria/):
$ meningotype --finetype --printseq <fasta1> <fasta2> <fasta3> ... <fastaN>
These are placed into a folder called printseq in the current directory.
To update the allele databases from http://pubmlst.org/neisseria/
$ meningotype.py --updatedb
A copy of the original database is saved to *.old just in case,
but is overwritten with each subsequent --updatedb.
Ensure you back up your old databases if you wish to keep them.
Kwong JC, Gonçalves da Silva A, Stinear TP, Howden BP, Seemann T.
meningotype: in silico typing for Neisseria meningitidis.
GitHub https://github.com/MDU-PHL/meningotype
- Software - submit via the GitHub issues page.
- Database - contact the pubmlst curator
- Jason Kwong (@kwongjc)
- Anders Gonçalves da Silva (@drandersg)
- Torsten Seemann (@torstenseemann)