CheckS: Checking the presence of a species in a metagenomics sample with known taxonomic composition

CheckS is a pipeline to check the presence of a species in NGS data (reads and assembled contigs) of a metagenomics sample, provided its reference genome and the reference genomes of the other known species.

CheckS carries out four analysis steps to determine the presence of a query reference genome as follows.

1. K-mer analysis
2. Coverage analysis
3. Assembly analysis
4. Gene analysis

Getting Started

Dependencies

CheckS requires Python 3.7 (tested on Python 3.7.4). You will need the following tools and python packages installed. Versions tested on are listed as well.

• Biopython - version 1.74
• DSK - version 2.3.3
• Minimap2 - version 2.18
• CoverM - version 0.6.1
• QUAST - version 5.0.2
• MetaGeneMark

Downloading CheckS

You can download the latest release of CheckS from Releases or clone the CheckS repository to your machine.

git clone https://github.com/Vini2/CheckS.git

If you have downloaded a release, you will have to extract the files using the following command.

unzip [file_name].zip

Now go in to the CheckS folder using the command

cd CheckS/

Setting up the environment

We recommend that you use Conda to run CheckS. You can download Anaconda or Miniconda which contains Conda.

Once you have installed Conda, make sure you are in the CheckS folder. Now run the following commands to create a Conda environment and activate it to run CheckS.

conda env create -f environment.yml
conda activate checks

You will have to download and setup MetaGeneMark from http://exon.gatech.edu/GeneMark/license_download.cgi. Next export the path to the MetaGeneMark folder.

export MGM_PATH=/path/to/MetaGeneMark_linux_64/mgm

Now you are ready to run CheckS.

If you want to switch back to your normal environment, run the following command.

conda deactivate

Using CheckS

You can see the usage options of CheckS by typing ./CheckS -h on the command line. For example,

usage: CheckS [-h] --contigs CONTIGS --reads1 READS1 --reads2 READS2
              --query_ref QUERY_REF --other_refs OTHER_REFS --output OUTPUT
              [--ref_ext REF_EXT] [--k K] [--similarity SIMILARITY]
              [--prefix PREFIX] [--nthreads NTHREADS] [-v]

CheckS is a pipeline to check the presence of a species in a metagenomics
sample, provided its reference genome and the reference genomes of the other
known species.

optional arguments:
  -h, --help            show this help message and exit
  --contigs CONTIGS     path to the contigs file
  --reads1 READS1       path to the forward reads file
  --reads2 READS2       path to the reverse reads file
  --query_ref QUERY_REF
                        path to the query reference genome
  --other_refs OTHER_REFS
                        path to the folder with other reference genomes
  --output OUTPUT       path to the output folder
  --ref_ext REF_EXT     extension of the reference genome files. [default:
                        fasta]
  --k K                 k value to run DSK k-mer counting. [default: 25]
  --similarity SIMILARITY
                        similarity threshold for mapping. [default: 0.9]
  --prefix PREFIX       prefix for the output file
  --nthreads NTHREADS   number of threads/cores to use. [default: 8]
  -v, --version         show program's version number and exit

Example Usage

./CheckS --contigs contigs.fasta --reads1 reads_1.fq --reads2 reads_2.fq --query_ref Klebsiella_variicola.fasta --other_refs Reference_Sequences/ --output /path/to/output/

References

[1] DSK: k-mer counting with very low memory usage. Rizk et al. Bioinformatics, Volume 29, Issue 5, 1 March 2013, Pages 652–653.

[2] CoverM - https://github.com/wwood/CoverM

[3] MetaQUAST: evaluation of metagenome assemblies. Mikheenko et al. Bioinformatics, Volume 32, Issue 7, 1 April 2016, Pages 1088–1090.

[4] Minimap2: pairwise alignment for nucleotide sequences. Li. Bioinformatics, Volume 34, Issue 18, 15 September 2018, Pages 3094–3100.

[5] Ab Initio Gene Identification in Metagenomic Sequences. Tang and Borodovsky. In: Nelson K. (eds) Encyclopedia of Metagenomics. Springer, New York, NY.