ECTyper is a standalone versatile serotyping module for Escherichia coli. It supports both fasta (assembled) and fastq (raw reads) file formats. The tool provides convenient species identification coupled to quality control module giving a complete, transparent and reference laboratories suitable report on E.coli serotyping.

• python >= 3.5
• bcftools >= 1.8
• blast == 2.7.1
• seqtk >= 1.2
• samtools >= 1.8
• bowtie2 >= 2.3.4.1
• mash >= 2.0

• biopython >= 1.70
• pandas >= 0.23.1
• requests >= 2.0

1. If you do not have conda environment, get and install miniconda or anaconda:

   bash miniconda.sh -b -p $HOME/miniconda
   echo ". $HOME/miniconda/etc/profile.d/conda.sh" >> ~/.bashrc
   source ~/.bashrc```
   
   

2. Install conda package from bioconda channel conda install -c bioconda ectyper

Second option is to install from the source.

1. Install dependencies. On Ubuntu distro run

apt install samtools bowtie2 mash bcftools ncbi-blast+ seqtk

1. Install python dependencies via pip:

pip3 install pandas biopython

1. Clone the repository or checkout a particular release (e.g v1.0.0, etc.):

git clone https://github.com/phac-nml/ecoli_serotyping.git
git checkout v1.0.0 #optionally checkout release version

1. Install ectyper: python3 setup.py install

1. Put the fasta/fastq files for serotyping analyses in one folder (concatenate paired raw reads files if you would like them to be considered a single entity)
2. ectyper -i [file path] -o [output_dir]
3. View the results on the console or in cat [output folder]/output.csv

• ectyper -i ecoliA.fasta for a single file
• ectyper -i ecoliA.fasta -o output_dir for a single file, results stored in output_dir
• ectyper -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna for multiple files (comma-delimited)
• ectyper -i ecoli_folder for a folder (all files in the folder will be checked by the tool)

usage: ectyper [-h] [-V] -i INPUT [-c CORES] [-opid PERCENTIDENTITYOTYPE]
               [-hpid PERCENTIDENTITYHTYPE] [-oplen PERCENTLENGTHOTYPE]
               [-hplen PERCENTLENGTHHTYPE] [--verify] [-o OUTPUT] [-r REFSEQ] [-s] [--debug]
               [--dbpath DBPATH]

ectyper v1.0 database v1.0 Prediction of Escherichia coli serotype from raw reads or assembled
genome sequences. The default settings are recommended.

optional arguments:
  -h, --help            show this help message and exit
  -V, --version         show program's version number and exit
  -i INPUT, --input INPUT
                        Location of E. coli genome file(s). Can be a single file, a comma-
                        separated list of files, or a directory
  -c CORES, --cores CORES
                        The number of cores to run ectyper with
  -opid PERCENTIDENTITYOTYPE, --percentIdentityOtype PERCENTIDENTITYOTYPE
                        Percent identity required for an O antigen allele match [default 90]
  -hpid PERCENTIDENTITYHTYPE, --percentIdentityHtype PERCENTIDENTITYHTYPE
                        Percent identity required for an H antigen allele match [default 95]
  -oplen PERCENTLENGTHOTYPE, --percentLengthOtype PERCENTLENGTHOTYPE
                        Percent length required for an O antigen allele match [default 95]
  -hplen PERCENTLENGTHHTYPE, --percentLengthHtype PERCENTLENGTHHTYPE
                        Percent length required for an H antigen allele match [default 50]
  --verify              Enable E. coli species verification
  -o OUTPUT, --output OUTPUT
                        Directory location of output files
  -r REFSEQ, --refseq REFSEQ
                        Location of pre-computed MASH RefSeq sketch. If provided, genomes
                        identified as non-E. coli will have their species identified using MASH.
                        For best results the pre-sketched RefSeq archive
                        https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh is
                        recommended
  -s, --sequence        Prints the allele sequences if enabled as the final columns of the
                        output
  --debug               Print more detailed log including debug messages
  --dbpath DBPATH       Path to a custom database of O and H antigen alleles in JSON format. Check
                        Data/ectyper_database.json for more information

ECTyper requires minimum options to run (-i and -o) but allows for extensive configuration to accomodate wide variaty of typing scenarios

To provide an easier interpretation of the results and typing metrics, following QC codes were developed. These codes allow to quickly filter "reportable" and "non-reportable" samples. The QC module is tightly linked to ECTyper allele database, specifically, MinPident and MinPcov fields. For each reference allele minimum %identity and %coverage values were determined as a function of potential "cross-talk" between antigens (i.e. multiple potential antigen calls at a given setting). The QC module covers the following serotyping scenarios. More scenarios might be added in future versions depending on user needs.

ECTyper capitalizes on a concise minimum output coupled to easy results interpretation and reporting. ECTyper v1.0 serotyping results are available in a tab-delimited output.tsv file consisting of the 16 columns listed below:

1. Name: Sample name (usually a unique identifier)
2. Species: the species column provides valuable species identification information in case of inadvertent sample contamination or mislabelling events
3. O-type: O antigen
4. H-type: H antigen
5. Serotype: Predicted O and H antigen(s)
6. QC: The Quality Control value summarizing the overall quality of prediction
7. Evidence: How many alleles in total used to both call O and H antigens
8. GeneScores: ECTyper O and H antigen gene scores in 0 to 1 range
9. AllelesKeys: Best matching ECTyper database allele keys used to call the serotype
10. GeneIdentities(%): %identity values of the query alleles
11. GeneCoverages(%): %coverage values of the query alleles
12. GeneContigNames: the contig names where the query alleles were found
13. GeneRanges: genomic coordinates of the query alleles
14. GeneLengths: allele lengths of the query alleles
15. Database: database release version and date
16. Warnings: any additional warnings linked to the quality control status or any other error message(s).

Selected columns from the ECTyper typical report are shown below.