I´m mapping a set of ont long reads to the human genome:
I´m using this genome version from gencode: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_33/GRCh38.p13.genome.fa.gz
See description here: https://www.gencodegenes.org/human/
I´m using a skin sample so i expect to find bacteria ... and fungi from Malazessia genus for exemple. But i get no hits since they are filtered when using minimap against the HG reference above.
I´m wondering how are you delaing with these false positives sequences (in such case fung) in human assemblies ??