Concept

This package has been written to help you:

1. generate a psudocontig starting from a draft genome (with Contiguator) -- it uses a reference genome as a template
2. do the variant calling against a reference genome (with mummer) -- it generates a .vrt file

Dependencies

• contiguator (NOTE: contiguator should be in the $PATH variable. This means that you should be able to type ./Contiguator.py and execute the command)
• mummer
• python (2.7)

Usage

1. First of all we need to create the Pseudocontig

vrtTools-generatePseudocontig.py example/H37Rv_mod.fasta example/00-R0025_denovo.fasta

CONTIGuator will create the folders Map_<id_reference> and UnMappedContigs!

NOTE: CONTIGuator is very picky about the identifiers inside your fasta file. In order to avoid problems, please remove all dots present in the identifier before running vrtTools-generatePseudocontig.py. A command that can help you this this is:

cat H37Rv.fasta |sed -e 's/\./_/' > H37Rv_mod.fasta

2. We can now align the reference and the Pseudocontig with mummer

vrtTools-runMummer.py example/H37Rv_mod.fasta Map_NC.000962.3/PseudoContig.fsa out_mummer

3. We can now convert the .snps file generated by mummer into a .vrt file

vrtTools-snps2vrt.py out_mummer.snps example/H37Rv_mod.fasta Map_NC.000962.3/PseudoContig.fsa ref_vs_00-R0025.vrt