This pipeline predicts essential genes from non-clonal bacterial samples.
It aligns your FastQ files with BWA-MEM, realigns indels and calls variants with LoFreq and annotates the resulting vcf-file with SNPeff.
The *genes.txt files from multiple samples can be used as input for
essential_genes_from_tables.py (also found in this folder) to
predict essential genes. Please contact Andreas Wilm
<mailto:wilma@gis.a-star.edu.sg> or Niranjan Nagarajan
<mailto:nagarajann@gis.a-star.edu.sg> regarding details for the
latter.
Your reference fasta file must match the given SNPeff genomes. Your genome of choice also has to be in the list of supported locally available databases, i.e. it might have to be downloaded first (please contact us to do so)
For admins: The command to use is java -jar $SNPEFFDIR/snpEff.jar download -c $SNPEFFDIR/snpEff.config -v $SPECIES. Also check first if
the reference genome in question contains the same sequences (dump -v -txt $genome).