目前常用的参考基因组主要有三个来源：

• Ensembl:ftp://ftp.ensembl.org/pub/
• UCSC:http://hgdownload.cse.ucsc.edu/downloads.html
• NCBI:ftp://ftp.ncbi.nih.gov/genomes/
  一般来说，需要下载的文件包括：fasta序列、GTF文件；

最常用的可以从Ensembl下载

hg38

genome fasta格式
wget ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz
注释 gtf格式
wget ftp://ftp.ensembl.org/pub/release-99/gtf/homo_sapiens/Homo_sapiens.GRCh38.99.chr.gtf.gz

mus_musculus

genome
wget ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz
gtf
wget ftp://ftp.ensembl.org/pub/release-99/gtf/mus_musculus/Mus_musculus.GRCm38.99.chr.gtf.gz

caenorhabditis_elegans

genome
wget ftp://ftp.ensembl.org/pub/release-99/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz
gtf
wget ftp://ftp.ensembl.org/pub/release-99/gtf/caenorhabditis_elegans/Caenorhabditis_elegans.WBcel235.99.gtf.gz