Creating reference genome that includes HIV genome

Question

[FrankStarling]

Hi all, In this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9831945/) the authors use a reference genome that includes the HIV genome. Seen in this sentence of the paper:

"Adapters and low-quality bases were trimmed using Cutadapt v1.18 software 11 before alignment with the human reference genome(hg38andHIV-1: NC_001802.1) and GENCODE annotation v30 using STAR 2.7.0f. 12"

Searching for NC_001802.1 directs to a page (https://www.genome.jp/dbget-bin/www_bget?refseq:NC_001802) that contains the complete HIV genome which is expected.

Thus my question is how might I go about integrating the HIV genome into my human reference genome. The paper linked above uses STAR but I prefer to use HISAT2 as it can easily run on a laptop. To do this using HISAT2 I believe I would have to combine the two genomes into one before building my indices. Any suggestions are appreciated.

Answer 1

[ATpoint]

Get both the human and viral genomes, both in fasta format, then use cat to combine both files. Technically speaking, in the merged genome fasta the viral genome is just another 'chromosome/contig'. Index that resulting file with whatever aligner you want to use.

[FrankStarling]

Thanks @atpoint.