Mapping, snps calling, phylogeny
- multiple_ariba.sh Runs ariba https://github.com/sanger-pathogens/ariba on multiple fastq files
- multiple_mappings_kabre.sh Aligns mutiple fastq files to a reference using bwa (https://github.com/lh3/bwa), call SNPs with bcftools (http://www.htslib.org/doc/bcftools.html), build a phylogenetic tree with RAXmL https://github.com/stamatak/standard-RAxML