ContaLocate

Bioinformatics / Genomics A tool to extract DNA segments with homogeneous olignonucleotide composition from a genome assembly.

• Learns a compositional profile for the host and the contaminant, previoulsy identified with i.e. PhylOligo.
• Generates a GFF3 map of the contaminant positions in the genome.

Once you have explored your assembly's oligonucleotide composition, identified and selected -potentially partial- contaminant material, use ContaLocate to target species-specific contaminant DNA according to a double parametrical threshold.

contalocate.R -i genome.fasta -r genome_host.fa -c genome_conta_1.fa 

The training set for the host genome can be omitted if the amount of contaminant is negligible. In this case, the profile of the host will be trained on the whole genome, including the contaminant.

contalocate.R -i genome.fasta -c genome_conta_1.fa 

The set up of the thresholds can be manually enforced. The user will interactively prompted to set the thresholds given the distribution of windows divergence.

contalocate.R -i genome.fasta -c genome_conta_1.fa -m

Parameters:

• -i --genome Multifasta of the genome assembly (required)
• -r --host_learn Host training set (optional)
• -c --conta_learn Contaminant training set (optional, but recommended^^) if missing and sliding window parameters are given, the sliding windows composition will be compared to the whole genome composition to contrast potential HGTs (prokaryotes and simple eukaryotes only)
• -t --win_step Step of the sliding windows analysis to locate the contaminant (optional) default: 500bp or 100bp
• -w --win_size Length of the sliding window to locate the contaminant (optional) default: 5000bp
• -d --dist Divergence metric used to compare profiles: (KL), JSD or Eucl
• -m --manual_threshold You will be asked to manually set the thresholds
• -h --help What it says

Install

• Dependencies:

  • Python 3.x
    • BioPython
    • Numpy
    • Cython
  • R 3.x
    • ape
    • getopt
    • gtools

• Install python3 and the latest R version according to your system

In the Bash/Shell, as root/admin if wanted installed globally.

#Ubuntu/Debian-based
apt-get install python3-dev python3-setuptools r-base
easy_install3 -U setuptools
pip3 install biopython 
pip3 install cython
pip3 install numpy

in R, as root or user

install.packages(c("ape","getopt","gtools"))

• clone the repo

https://github.com/itsmeludo/ContaLocate.git

• Link the programs into a directory listed in your $PATH

cd ContaLocate
sudo ln -s `pwd`/{contalocate.R,Kount.py} /usr/local/bin/