Corer

Sequence-based Pangenomic Core Detection

• k-mer-based detection of a pangenome's core
• Assembled genomes or reads as input
• Customized core definition
• Low demands in run time and memory

Publication

Schulz, T., Wittler, R., Stoye, J.: Sequence-based pangenomic core detection. iScience. (2022)

Table of Contents

• Requirements
• Compilation
• Usage
• Test data
• Evaluation workflow
• FAQ
• Contact
• Licenses
• Privacy

Requirements

Corer identifies the core of a given pangenome represented as a compacted, colored de Bruijn graph using the API of Bifrost (version 1.2.1 or higher). Apart from the requirements of Bifrost (c++ and cmake), there are no further strict dependencies.

A provided evaluation workflow requires snakemake, and the packages Biopython and matplotlib to be installed on your system.

Compilation

cd <corer_directory>/src
make

By default, the installation creates:

• a binary (Corer)

You may want to make the binary accessible via your PATH variable.

Please note the installation instructions regarding the default maximum k-mer size of Bifrost from its README. E.g., if your Bifrost libraries have been compiled to support a k-mer length of up to 63, change Corer's makefile accordingly (add -DMAX_KMER_SIZE=64 to CFLAGS).

If during the compilation, the Bifrost library files are not found, make sure that the corresponding folder is found as include path by the C++ compiler. You may have to add -I/usr/local/include (with the corresponding folder) to CFLAGS in the makefile.

Usage:

Corer

displays the command line interface:

Corer [-hs] [-q QUORUM] [-d DELTA] [-i Graph_File_Prefix] [-o Output_File_Prefix] [-t Nb_Threads]

Extracting a pangenome's core.

Required parameters:
   -i   --igraph  Input graph file prefix
   -o   --ograph  Output graph file prefix

Optional parameters with required argument:
   -q   --quorum   Absolute quorum defining the core (default is 90% of pangenome size)
   -d   --delta    Maximum distance between core k-mers (default is 50)
   -t   --threads  Number of threads (default is 1)

Optional parameters without argument:
   -s   --snippets  Output unitig core snippets to stdout
   -h   --help      Display this help message

Examples

1. Get some testing data

   You may want to get some toy data first to try out the program.

   wget 'https://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/bigZips/160sequences.tar.gz'
   tar xvzf 160sequences.tar.gz
   

   These commands let you download and unpack a small dataset of 160 individual samples of different Ebola virus subspecies.

2. Create a pangenome graph

   Corer requires a Bifrost graph to perform a core prediction. First, create an input file list for Bifrost, e.g., by running

   ls -l *.fa | tr -s ' ' | cut -d' ' -f9 > list.txt
   

   In order to build the actual graph use Bifrost.

   path/to/bifrost/bin/Bifrost build -r list.txt -o ebolaPangenome -c
   

3. Predict the core

   Once the graph has been built, Corer can predict its core. The command

   Corer -i ebolaPangenome -o ebolaCore -q 128 -d 60
   

   predicts a core for the ebola pangenome, where a core k-mer needs to occur in at least 128 genomes and the maximum distance between two core k-mers is 61.

Test data

Test data can be downloaded from public databases.

1. Prokaryotic data sets

   Four prokaryotic pangenomes may be downloaded from NCBI. Accession numbers can be found in the directory experiments.

2. Arabidopsis pangenome

   Assemblies of 18 accessions of Arabidopsis thaliana can be downloaded here.

   Corresponding read data sets for 17 of the above assemblies are available here.

Evaluation workflow

The directory experiments contains an evaluation workflow that may be executed using snakemake.

For execution of the workflow, proceed as follows:

• Install all programs to be tested on your system.

• Install gene annotation pipelines (prokka for prokaryotic and Augustus for eukaryotic data sets).

• Install all tools needed for subsequent analyses.

• Download the testing data.

• Place your testing data into the provided subdirectories and add the locations of program binaries and other dependencies into the configuration file experiments/config.yaml:

  # PLEASE ADJUST THE FOLLOWING PARAMETERS --------------------------------------
  
  #Program binaries that shall be used
   corer_bin: "../src/Corer"
   panaroo_bin: "/path/to/panaroo/bin"
   sibeliaz_bin: "/path/to/sibeliaz/bin"
   #Program binaries of gene annotation softwares
   prokka_bin: "/path/to/prokka/bin"
   augustus_bin: "/path/to/augustus/bin"
   #Bifrost binary that shall be used
   bifrost_bin: "/path/to/bifrost/bin"
   #Blastn binary that shall be used
   blastn_bin: "/path/to/blastn/bin"
   #Makeblastdb binary that shall be used
   makeblastdb_bin: "/path/to/makeblastdb/bin"
   #Path to BUSCO analysis script
   BUSCOscript: "/path/to/BUSCO/script.py"
   #Brassicales BUSCO database directory
   BUSCObrasDB: "/path/to/db/dir"
  
  
  #------------------------------------------------------------------------------
  ...
  

• Change into directory experiments and run the workflow.

  cd experiments
  snakemake
  

FAQ

We recommend to have a look at the FAQs of Bifrost.

Contact

For any question, feedback or problem, please feel free to file an issue on GitHub or contact the developers and we will get back to you as soon as possible.

Corer is provided as a service of the German Network for Bioinformatics Infrastructure (de.NBI). We would appriciate if you would participate in the evaluation of Corer by completing this very short survey.

Licenses

• The hash function library xxHash is BSD licensed (https://github.com/Cyan4973/xxHash)

• The popcount library is BSD licensed (https://github.com/kimwalisch/libpopcnt)

• The libdivide library is zlib licensed (https://github.com/ridiculousfish/libdivide)

• The kseq library is copyrighted by Heng Li and released under the MIT license (http://lh3lh3.users.sourceforge.net/kseq.shtml)

• The CRoaring library is Apache 2.0 licensed (https://github.com/RoaringBitmap/CRoaring)

• Bifrost is BSD-2 licensed (https://github.com/pmelsted/bifrost)

• Corer is GNU GPLv3 licensed LICENSE

Privacy

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