General question smaller contigs

ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation

Apache License 2.0

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General question smaller contigs #75

Open mdabalkey opened 4 years ago

mdabalkey commented 4 years ago

Hello,

Could you please let me know what FastANI does with contigs less than 500 bp? Does it remove them and start working with 3kb contigs?

Thanks!

cjain7 commented 4 years ago

Yes, contigs less than 500 bp are ignored. By default, only contigs above 3 kbp are considered. From the help page, please check the parameters. You should be able to tune this parameter to a certain extent. Having said that, reducing this threshold would also affect the total runtime.