Overview

vk genome location [<path>]
vk genome list
vk genome --search=<term>
vk genome ncbi [options] --ref=<asm_name> [--accession-chrom-names]
vk genome wormbase [options] --ref=<asm_name>

The genome command can be used to download and prepare reference genomes for use with other tools within vcf-kit. vcf-kit will do the following when downloading a reference genome:

  1. Download the reference genome.
  2. If downloaded from NCBI, vcf-kit will attempt to replace chromosomes names with shorthand descriptors of if possible (e.g. Chromosome I).
  3. Unzip the gzipped reference and re-compress using bgzip.
  4. Create a bwa index.
  5. Create a samtools index.
  6. Create a blast database.
  7. Remove temporary file names.

Usage

View/set genome directory

By default, genomes are stored within your home directory in a .genome folder. The location of this directory can be viewed by typing:

vk genome location

Tip

You can use a bash alias to access the genome currently set with vcf-kit. Add this to your .bash_profile: alias GENOME=`vk genome location` And you can access the currently set genome using GENOME.

Additionally, you can change the location by adding a path:

vk genome /path-to-my-new-genome-directory

List genomes

A list of downloaded genomes can be viewed using:

vk genome list

Download Genomes

Search NCBI

vcf-kit makes it easy to obtain and prepare genomes from the NCBI genome database. To do this, it downloads a text file containing a list of all available genomes and uses this for searching purposes. To search for a genome, you can type:

vk genome --search="Human cyclovirus"

The results of the search will be output in a table:


  Genome Directory: /Users/dancook/.genome


  Searching...

    assembly_accession    bioproject    organism_name               asm_name         ...
    --------------------  ------------  --------------------------  ---------------  ...
    GCF_000908835.1       PRJNA209365   Human cyclovirus VS5700009  ViralProj209365  ...
    GCF_000918035.1       PRJNA243497   Human cyclovirus            ViralProj243497  ...

  To download a genome and setup for use:

    vk genome --ref=<asm_name>

As the instructions illustrate, you can download the genome by providing the asm_name (assembly name).

Download from NCBI

Set --ref to an asm_name from the search results table to download a genome.

vk genome --ref=ViralProj209365

Wormbase

Reference genomes can also be obtained from wormbase. 

vk genome wormbase --ref=WS245

Custom Directories

It is possible to set the directory to download a genome using the --directory parameter. This command will set the directory to the current location.

vk genome ncbi --directory="." --ref=ViralProj15089