search

PierreBSC / Viral-Track

MIT License
54 stars 27 forks source link

Downloading fasta files for host genome #29

Closed malonzm1 closed 10 months ago

malonzm1 commented 10 months ago

Hi,

Sorry if the answer is obvious. Do I have to download all the fasta files in https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/ for the human host genome? Or can I just use Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz? Or can I use another GRCh38 genome fasta file (all chromosomes in one fasta file)?

Thanks and good day.

PierreBSC commented 10 months ago

Hi,

I would strongly recommend using all the different fast files, first to improve the performance and second because Viral-Track is parametrised to remove all reads mapped to the host genome (names of the chromosomes to remove are pre-defined...) Hope this helps, Best, Pierre