Charlie Seto

Commands: I rolled my own R1 and R2.fastq and pulled files from the dropbox. First: bwa index /home1/cseto/StrainFinderFiles/all.amphora_genes.fst python 0.run.py --fastqs list --ref /home1/cseto/StrainFinderFiles/all.amphora_genes.fst --map /home1/cseto/StrainFinderFiles/bact.meta.txt bwa mem -a /home1/cseto/StrainFinderFiles/all.amphora_genes.fst...

When using the example_files that come with the github: python 0.run.py --fastqs ./AMPHORA/list --ref ./example_files/ref.fasta --map ./example_files/map.txt bwa mem -a ./example_files/ref.fasta One.fastq > One.sam bwa mem -a ./example_files/ref.fasta Two.fastq >...