Package: mashpit
MashpitCreate a database of mash signatures and find the most similar genomes to a target sampleInstallationInstall sratoolkit for Linuxwget 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/binInstall mashpit using pip:pip install mashpitOr manually install after git clone:git clone https://github.com/tongzhouxu/mashpit.git
python setup.py installNgstool is needed to build mashpit database on Raspberry Pi:Build and install ngs. Follow instructions athttps://github.com/ncbi/ngs/wiki/Building-and-Installing-from-SourceInstall ncbi-vdb. Follow instructions athttps://github.com/ncbi/ncbi-vdb/wiki/Building-and-Installing-from-SourceBuild and install ngstools from source. Follow instructions athttps://github.com/ncbi/ngs-toolsDependenciesPython >= 3.8Sratoolkit 2.10.8Mashpit DatabaseA mashpit database is a directory containing:$DB_NAME.db$DB_NAME.sigTwo types of Mashpit database:Standard Database (Pathogen Detection Database)A standard database is a collection of representative genomes from each cluster onPathogen Detection. By default mashpit will download the latest version of a specified species and find the centroid of each SNP cluter (SNP tree).Custom DatabaseA custom database is a collection of genomes based on a proveded biosample accesion list or a keyword.Usage0. 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 keyExample commandmashpit config example@example.com -k your_passwordMore information about Entrez API key can be found onthis page.1. Build the databaseusage: 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 keywordExample commandmashpit build standard salmonella -s Salmonellamashpit build biosample_list db_name -l file.listmashpit build keyword db_name -t salmonella_enteritidis2. Sketch the genomesusage: 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 exitExample commandmashpit sketch db_name3. Run a queryusage: 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 exitExample commandmashpit query sample.fasta db_name