tseemann
commented
4 years ago Answer: Use snippy-multi from snippy package. This is also done by nullarbor.
Googling information on the web and reading SeqAnswers, Biostars, and github is how most bioinformticians learn their craft. Our field is always changing, so it is a key, and necessary skill.
SNP "thresholds" are risky and will be different for different organisms. eg. M.tb vs E.coli
Can anyone advice me how to generate multiple alignment fasta from raw fastq? I have 400+ isolates and trying to generate a SNP distance matrix (none mash) to check for epidemiological link. i.e SNP coverage distance less than 12 SNPs between isolates and plot into a tree.. can anyone point me to a correct info? newbie in bioinformatics and as usual most of the time supervisor is not free all the time. I ended have to find info from the web and learn it that way. Any help will be greatly appreciated.