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ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
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Testing how FastANI handles reverse complemented sequence #59

Open cindy-tu opened 4 years ago

cindy-tu commented 4 years ago

Hello,

Just a minor question. I was curious in terms of how FastANI handles reverse complemented sequence. I would hypothesize that FastANI would detect it no problem since BLAST is able to detect reverse complements just fine.

I have attached a ZIP file with a sequence file (query.fasta) and another file with the reverse complement of it (query_rc.fasta). The sequences are 130kb in length. I'm using FastANI1.3.

fastANI -q query.fasta -r query_rc.fasta --fragLen 1500 -o rc.out -t 4

The result is an ANI of 99.9998 with 87/87 fragments aligned. I'm just wondering why it is not 100 since the sequences are identical just reverse complemented.

Input.zip

Thank you!

cjain7 commented 4 years ago

FastANI considers canonical k-mers (i.e., minimum of k-mer and its reverse complement). You can know more through source code (link to function).

Not sure why the output is different though..