Salmonella Outbreak Project

Instructions

Detected K-mers are stored in a hash table (python dictionary) for each strain, where the key is the k-mer and the value is the number of occurrences in the full file. The number of occurrences of each k-mer can therefore be accessed in constant time.

python main.py -p data/salmonella-enterica.reads.fna data/salmonella-enterica-variant.reads.fna -k 50 -t 10 -v

Command line interface

usage: main.py [-h] [-p PATH PATH] [-f [FORMAT]] [-k [K]]
               [-t [FILTERING_THRESHOLD]] [-d [DISTANCE_THRESHOLD]] [-v] [-s]
               [-l]

SNP detector

optional arguments:
  -h, --help            show this help message and exit
  -p PATH PATH, --path PATH PATH
                        Paths to FASTA files (or to stored binary files if -l)
  -f [FORMAT], --format [FORMAT]
                        Sequencing file format for Biopython
  -k [K]                Length of k-mers
  -t [FILTERING_THRESHOLD], --filtering-threshold [FILTERING_THRESHOLD]
                        Threshold for k-mers filtering
  -d [DISTANCE_THRESHOLD], --distance-threshold [DISTANCE_THRESHOLD]
                        Threshold for Levenshtein distance
  -v, --visualize       Plot intermediate results
  -s, --save            Save collected k-mers
  -l, --load            Load collected k-mers

If the filtering-threshold argument is not provided, user is interactively asked to input a value during execution.

Storing and loading dictionaries

Interface is provided to store/load the dictionary of detected k-mers in/from binary files using pickle. This allows to test different thresholds for the filters, detecting the k-mers only once and saving time.

Warning: the resulting binary files can be huge.

Store

To store the dictionaries computed in the run:

python main.py -p data/salmonella-enterica.reads.fna data/salmonella-enterica-variant.reads.fna -k 20 -v -s

This will create two binary files, called data/salmonella-enterica.reads_20.pickle and data/salmonella-enterica-variant.reads_20.pickle (20 as the provided k).

Load

To load a previously stored binary file:

python main.py -p data/salmonella-enterica.reads_20.pickle data/salmonella-enterica-variant.reads_20.pickle -k 20 -v -l

Data

Data is not included in this repo, please download it from the course website. A sample file for testing can be found here.

COVID-19 sequences can be downloaded from the COVID-19 Data Portal, looking for entries for which raw reads are available. For example, Illumina reads for lineages B.1.1.7 and B.1.1.8 can be respectively downloaded here and here.

Authors

The project is presented by the CEO, CTO and CHO of DZA Computing:

• Sophie Zhang
• Enrico Agrippino
• Gabriele Degola

© 2021 DZA Computing. All rights reserved.