how to make query list and reference list of genome in fastANI tool

Question

[biotechpedia]

could anyone elaborate how to make query list and reference list in fastANI tool, i could get output ANI for single query and single reference genome, but when i try for multiple ref and query genomes, my command is $ ./fastANI -q 119.fasta --rl Xac29-1.fasta Xanthomonas_albilinneans.fasta Xanthomonas_ arbicola.fasta -o punicae.text

it shows error as follows, 1, Misplaced option '-r' detected. All option have to be BEFORE the first argument 2, Misplaced option '-o' detected. All option have to be BEFORE the first argument

Answer 1

[Nay Catina Dia]

Hello, I don't know if you're still looking for an answer but here goes!

Your reference list and your query list should be text files containing the names (file names) of your .fasta genomes, one genome per line. For example, if you have three genomes gen1.fasta, gen2.fasta and gen3.fasta and you want a fastANI of many to many, then in both reflist.txt and querylist.txt you copy paste the following:
gen1.fasta
gen2.fasta
gen3.fasta

Your code will look like this:

fastANI --threads 2 --ql querylist.txt  --rl reflist.txt --matrix -o fastani.out

In your working directory you will need the query and referent lists and your genomes in fasta format. Hope that helps! Cheers, dian