Scripts for K. pnuemo isolate assembly paper
annotate_process.R -> annotate genomes with prokka, rgicard, BLAST using CARD, BLAST with specific target seqs and MLST typing
assemble_aws.R -> assemble genomes with canu (nanopore), spades (Illumina) using an AWS EC2 instance
assembe_process.R -> extract fasta from nanopore data, run assembly (if locally), run a round of pilon
assembly_compare.sh -> compare assemblies with nucmer and make dotplot
count_snps.R -> taking output from parsnp, count number of snps per sample
coverage_align.R -> get coverage per sample for nanopore or illumina data
parsnp.sh -> parsnp scripts (parsnp is part of HarvestTools)
pilon_loop_plot.R -> plot differences according to rounds of pilon
pilon_loop.R -> run multiple pilon loops to get as correct as possible
tree.R -> generate tree comparisons for all samples using parsnp