mashpit 0.9.2

A sketch-based surveillance platform

Mashpit

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

Installation

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

Install mashpit using pip:

pip install mashpit

Or manually install after git clone:

git clone https://github.com/tongzhouxu/mashpit.git
python setup.py install 

Ngstool is needed to build mashpit database 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 >= 3.8
• Sratoolkit 2.10.8

Mashpit Database

A mashpit database is a directory containing:

• $DB_NAME.db
• $DB_NAME.sig

Two types of Mashpit database:

1. Standard Database (Pathogen Detection Database)

   A standard database is a collection of representative genomes from each cluster on Pathogen Detection. By default mashpit will download the latest version of a specified species and find the centroid of each SNP cluter (SNP tree).

2. Custom Database

   A custom database is a collection of genomes based on a proveded biosample accesion list or a keyword.

Usage

0. Set up Entrez email and API key (For custom database only)

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 your_password

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

1. Build the database

usage: mashpit build [-h] [-s SPECIES] [-l LIST] [-t TERM]
                     {standard,biosample_list,keyword} name

Build mashpit database

positional arguments:
  {standard,biosample_list,keyword}
                        Database type: standard or custom
  name                  Mashpit database name

optional arguments:
  -h, --help            show this help message and exit
  -s SPECIES, --species SPECIES
                        Query keyword
  -l LIST, --list LIST  File containing a list of biosample accessions
  -t TERM, --term TERM  Query keyword

• Example command

mashpit build standard salmonella -s Salmonella

mashpit build biosample_list db_name -l file.list

mashpit build keyword db_name -t salmonella_enteritidis

2. Sketch the genomes

usage: mashpit sketch [-h] name

Build sketches for the records in the database

positional arguments:
  name        Mashpit database name

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

• Example command

mashpit sketch db_name

3. Run a query

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

Find the most similar assemblies to the target sample

positional arguments:
  sample                file name of the query sample
  database              name of the database

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

• Example command

mashpit query sample.fasta db_name