tongzhouxu / mashpit

:pencil: Sketch-based surveillance platform

Mashpit

Create a database of mash signatures and find the most similar genomes to a target sample. To contribute, please see the contributing guidelines here.

Installation

Option 1. Install with Conda/Mamba (Recommended)

conda create -n mashpit -c conda-forge -c bioconda 'mashpit=0.9.6'
conda activate mashpit

Option 2. Install with pip

1. Dependency: Install NCBI datasets

curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets'
chmod +x datasets
export PATH=$PATH:$PWD

2. Install mashpit using pip:

pip install mashpit

Or git clone from github:

git clone https://github.com/tongzhouxu/mashpit.git
cd mashpit
pip install . 

Mashpit Database

A mashpit database is a directory containing:

• $DB_NAME.db
• $DB_NAME.sig

Mashpit database can be built using:

1. A taxonomic name 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. BioSample accessions
   A custom database is a collection of genomes based on a proveded biosample accesion list.

Usage

1. Build a mashpit database

usage: mashpit build [-h] [--quiet] [--number NUMBER] [--ksize KSIZE] [--species SPECIES] [--email EMAIL] [--key KEY] [--pd_version PD_VERSION] [--list LIST] {taxon,accession} name

positional arguments:
  {taxon,accession}     mashpit database type.
  name                  mashpit database name

optional arguments:
  -h, --help            show this help message and exit
  --quiet               disable logs
  --number NUMBER       maximum number of hashes for sourmash, default is 1000
  --ksize KSIZE         kmer size for sourmash, default is 31
  --species SPECIES     species name
  --email EMAIL         Entrez email
  --key KEY             Entrez api key
  --pd_version PD_VERSION
                        a specified Pathogen Detection version (PDG accession). Default is the latest.
  --list LIST           Path to a list of NCBI BioSample accessions

• Example command

mashpit build taxon salmonella --species Salmonella

Note: Supported species names can be found in this list

2. Query against a mashpit database

usage: mashpit query [-h] [--number NUMBER] [--threshold THRESHOLD] [--annotation ANNOTATION] sample database

positional arguments:
  sample                path to query sample
  database              path to the database folder

optional arguments:
  -h, --help            show this help message and exit
  --number NUMBER       number of isolates in the query output, default is 200
  --threshold THRESHOLD
                        minimum jaccard similarity for mashtree, default is 0.85
  --annotation ANNOTATION
                        mashtree tip annoatation, default is none

• Example command

mashpit query sample.fasta path/to/database

Optional: Update the database

usage: mashpit update [-h] [--metadata METADATA] [--quiet] database name

positional arguments:
  database             path for the database folder
  name                 database name

optional arguments:
  -h, --help           show this help message and exit
  --metadata METADATA  metadata file in csv format
  --quiet              disable logs

• Example command

mashpit update path/to/database salmonella

Webserver

A local host webserver can be started using:

mashpit webserver