mashpit 0.8.1

A sketch-based surveillance platform

Mashpit

Create a database of mash signatures and find the most similar genomes to a target sample

Installation

• Sra-tools for Linux

  wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.10.8/sratoolkit.2.10.8-centos_linux64.tar.gz -O /tmp/sratoolkit.tar.gz
  

  tar -xvf /tmp/sratoolkit.tar.gz
  

  Add sratoolkit to the environment:

  export PATH=$PATH:$PWD/sratoolkit.2.10.8-centos_linux64/bin
  

• Mashpit can be downloaded using pip or conda:

  pip install mashpit
  

• Ngstool is needed to run mashpit on Raspberry Pi

  1. Build and install ngs. Follow instructions at https://github.com/ncbi/ngs/wiki/Building-and-Installing-from-Source
  2. Install ncbi-vdb. Follow instructions at https://github.com/ncbi/ncbi-vdb/wiki/Building-and-Installing-from-Source
  3. Build and install ngstools from source. Follow instructions at https://github.com/ncbi/ngs-tools

Dependencies

• Python 3.7 and 3.8
• Sra-tools 2.10.8

Usage

1. Create the database

usage: mashpit create [-h] database

Create new mashpit database

positional arguments:
  database    Name for the database.

optional arguments:
  -h, --help  show this help message and exit

• Example command

mashpit create reading

2. Set up Entrez email and API key

usage: mashpit config [-h] [-k KEY] email

Add Entrez email and key to environment variables

positional arguments:
  email              Entrez email address

optional arguments:
  -h, --help         show this help message and exit
  -k KEY, --key KEY  Entrez api key

• Example command

mashpit config [e-mail] -k p@$$word

More information about Entrez API key can be found on this page.

3. Collect the metadata

usage: mashpit metadata [-h] [-l LIST] [-t TERM]
                        database {bioproject_list,biosample_list,keyword}

Collect metadata from NCBI based on bioproject/biosample accession or keywords

positional arguments:
  database              Name of the database
  {bioproject_list,biosample_list,keyword}
                        Metadata collecting method. Available options:
                        bioproject_list, biosample_list, keyword

optional arguments:
  -h, --help            show this help message and exit
  -l LIST, --list LIST  File name of a list of bioproject or biosample
  -t TERM, --term TERM  Query keyword

• Example command
  • Using BioProject list

  mashpit metadata reading bioproject_list -l list_file
  

  • Using BioSample list

  mashpit metadata reading biosample_list -l list_file
  

  • Using keyword

  mashpit metadata reading keyword -t salmonella_reading
  

4. Get the assembly and the signature file for all the entries in the database

usage: mashpit sketch [-h] [-n NUMBER] database

Build sketches for the records in the database

positional arguments:
  database              Name of the database

optional arguments:
  -h, --help            show this help message and exit
  -n NUMBER, --number NUMBER
                        Number of genomes in a batch to be downloaded and
                        sketched. Default is 1000.

• Example command

mashpit sketch reading

5.Split the large signature file into separate ones to speed up the query

usage: mashpit split [-h] [-n NUMBER] database

Split large signature file to speed up the query

positional arguments:
  database              Name of the database

optional arguments:
  -h, --help            show this help message and exit
  -n NUMBER, --number NUMBER
                        Number of files to be splited into. Default is 16.

• Example command

mashpit split reading -n 16

6. Query in the database

usage: mashpit query [-h] [-n NUMBER] [-f] sample database

Find the most similar assemblies to the target sample

positional arguments:
  sample                target sample file path
  database              name of the database

optional arguments:
  -h, --help            show this help message and exit
  -n NUMBER, --number NUMBER
                        number of separated signature file
  -f, --force           overwrite query record if query table exists

• Example command

mashpit query sample_file reading -n 16