Precise inference of bacterial recombinations
recognise (recombinations in genomic sequences) has been developed for the identification of recombinations in haploid genome sequences where the recipient (and donor) are known.
Recombinations can be inferred with either Gubbins, when the donor is unknown, or 3seq, where the donor is known.
The input is either a two-column list of de novo assemblies (sample name and file path), or an alignment of sequences to the recipient (all in FASTA format). The recipient genome sequence is essential.
To use a list of recombinant assembly names, an example command is:
recognise --recipient ./data/AE007317.1.fasta --donor ./data/FQ312027.1.fasta --recombinant-list ./data/three_recombinants.list --output one_multifasta_recombinant_no_donor_test --method 3seq
To use an input alignment, an example command is:
recognise --recipient ./data/AE007317.1.fasta --donor ./data/FQ312027.1.fasta --aln-input ./data/recipient_donor_recombinant.aln --output one_multifasta_recombinant_no_donor_test --method 3seq
The software can be installed through cloning the repository and creating a conda environment:
git clone https://github.com/nickjcroucher/recognise
conda env create -f environment.yml
cd recognise
python setup.py install
This software is under active testing and development, please do not trust it for publication-level results at the moment.