GOMA pipeline - accessory files

Data files used in the GOMA pipeline to analyse M. tuberculosis WGS data. To ensure compatibility with all used software the name of the chromosome in all files has been changed to "Chromosome". The reference genome corresponds to the inferred nucleotide sequence of the Mycobacterium tuberculosis complex most recent common ancestor based on the chromosome of H37Rv (Comas et al., 2010; Nature Genetics (doi:10.1038/ng.590); Cole et al., 1998; NC_000962.3). The annotation files are based on the NCBI NC_000962.3 annotation in Genbank format (genes.chromosome.gff3) and a custom interval annotation file (additional_annotations_chromosome.bed) to annotate variants linked to essential genes (DeJesus et al., 2017), drug-resistance (Walker et al., 2015) and functional categories from MycoBrowser (Kapopoulou et al., 2011). The M. cannetti VCF is public under the accession number ERR313115.