Where to download GRCh38_no_alt_decoy reference fasta file?

Question

[gracie]

Hello,

Where can I get the GRCh38_no_alt_decoy reference fasta file; used to generate bowtie index files here: https://benlangmead.github.io/aws-indexes/bowtie?

Answer 1

[GenoMax]

From link provided in the table you linked: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/

[gracie]

hs38d1 is the decoy?

[GenoMax]

Yes.

NOTE: 22 February 2016 A new analysis set was released that combines the human decoy sequences from hs38d1 (GCA_000786075.2) with the GRCh38 "no alt" analysis set.