主要包括：
1，对应物种的基因组序列
2，对应物种基因组注释信息
3，比对软件对应的基因组索引文件
其中1和3二选一就可以，因为最后需要的是基因组索引文件，索引文件是由比对软件利用基因组序列构建而来。所以
如果下载的是索引文件，就不需要自己构建了，直接使用就可以了。
如果下载的是基因组序列，需要自己先构建索引文件。
1，基因组序列：
NCBI：
https://www.ncbi.nlm.nih.gov/genome/?term=
输入物种的英文名：human，就可以检索到相应物种的基因组信息还有基因组注释文件。
Fig1.png
选择Download sequences in FASTA format for genome
还可以下载转录本，蛋白序列。
EBI：
选择需要的物种名称，就会转到相应网页
http://asia.ensembl.org/index.html
右侧Download FASTA
Fig2.png
Fig3.png
2，基因组注释文件：
NCBI：
与上述基因组在同一页面
点击Download genome annotation in GFF，或右侧FTP Human annotation (GFF)。
Fig4.png
GCF_000001405.38_GRCh38.p12_genomic.gff.gz
##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build GRCh38.p12
#!genome-build-accession NCBI_Assembly:GCF_000001405.38
#!annotation-source NCBI Homo sapiens Annotation Release 109
##sequence-region NC_000001.11 1 248956422
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi? id=9606
NC_000001.11 RefSeq region 1 248956422 . + . ID=NC_000001.11:1..248956422;Dbxref=taxon:9606;Name=1;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA
NC_000001.11 BestRefSeq pseudogene 11874 14409 . + . ID=gene-DDX11L1;Dbxref=GeneID:100287102,HGNC:HGNC:37102;Name=DDX11L1;description=DEAD/H-box helicase 11 like 1;gbkey=Gene;gene=DDX11L1;gene_biotype=transcribed_pseudogene;pseudo=true
NC_000001.11 BestRefSeq transcript 11874 14409 . + .
ID=rna-NR_046018.2;Parent=gene-DDX11L1;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;Name=NR_046018.2;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2
NC_000001.11 BestRefSeq exon 11874 12227 . + . ID=exon-NR_046018.2-1;Parent=rna-NR_046018.2;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HG NC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2
NC_000001.11 BestRefSeq exon 12613 12721 . + . ID=exon-NR_046018.2-2;Parent=rna-NR_046018.2;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2
NC_000001.11 BestRefSeq exon 13221 14409 . + . ID=exon-NR_046018.2-3;Parent=rna-NR_046018.2;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2
NC_000001.11 BestRefSeq pseudogene 14362 29370 . - .
ID=gene-WASH7P;Dbxref=GeneID:653635,HGNC:HGNC:38034;Name=WASH7P;description=WAS protein family homolog 7 pseudogene;gbkey=Gene;gene=WASH7P;gene_biotype=transcribed_pseudogene;gene_synonym=FAM39F,WASH5P;pseudo=true
NC_000001.11 BestRefSeq transcript 14362 29370 . - .
ID=rna-NR_024540.1;Parent=gene-WASH7P;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;Name=NR_024540.1;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1
NC_000001.11 BestRefSeq exon 29321 29370 . - . ID=exon-NR_024540.1-1;Parent=rna-NR_024540.1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1
NC_000001.11 BestRefSeq exon 24738 24891 . - . ID=exon-NR_024540.1-2;Parent=rna-NR_024540.1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 :
ref_GRCh38.p12_top_level.gff3.gz
##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build GRCh38.p12
#!genome-build-accession NCBI_Assembly:GCF_000001405.38
#!annotation-date 26 March 2018
#!annotation-source NCBI Homo sapiens Annotation Release 109
##sequence-region NC_000001.11 1 248956422
##species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi? id=9606
NC_000001.11 RefSeq region 1 248956422 . + . ID=id0;Dbxref=taxon:9606;Name=1;chromosome=1;gbkey=Src;genome=chromosome;mol_type=genomic DNA
NC_000001.11 BestRefSeq pseudogene 11874 14409 . + .
ID=gene0;Dbxref=GeneID:100287102,HGNC:HGNC:37102;Name=DDX11L1;description=DEAD/H-box helicase 11 like 1;gbkey=Gene;gene=DDX11L1;gene_biotype=transcribed_pseudogene;pseudo=true
NC_000001.11 BestRefSeq transcript 11874 14409 . + .
ID=rna0;Parent=gene0;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;Name=NR_046018.2;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2
NC_000001.11 BestRefSeq exon 11874 12227 . + . ID=id1;Parent=rna0;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2
NC_000001.11 BestRefSeq exon 12613 12721 . + . ID=id2;Parent=rna0;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2
NC_000001.11 BestRefSeq exon 13221 14409 . + . ID=id3;Parent=rna0;Dbxref=GeneID:100287102,Genbank:NR_046018.2,HGNC:HGNC:37102;gbkey=misc_RNA;gene=DDX11L1;product=DEAD/H-box helicase 11 like 1;transcript_id=NR_046018.2
NC_000001.11 BestRefSeq pseudogene 14362 29370 . - .
ID=gene1;Dbxref=GeneID:653635,HGNC:HGNC:38034;Name=WASH7P;description=WAS protein family homolog 7 pseudogene;gbkey=Gene;gene=WASH7P;gene_biotype=transcribed_pseudogene;gene_synonym=FAM39F,WASH5P;pseudo=true
NC_000001.11 BestRefSeq transcript 14362 29370 . - .
ID=rna1;Parent=gene1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;Name=NR_024540.1;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1
NC_000001.11 BestRefSeq exon 29321 29370 . - . ID=id4;Parent=rna1;Dbxref=GeneID:653635,Genbank:NR_024540.1,HGNC:HGNC:38034;gbkey=misc_RNA;gene=WASH7P;product=WAS protein family homolog 7 pseudogene;transcript_id=NR_024540.1
EBI：
与上述基因组在同一页面
Fig5.png
文件一般命名
<species>.<assembly>.<version>.gtf.gz
<species>: The systematic name of the species.
<assembly>: The assembly build name.
<version>: The version of Ensembl from which the data was exported.
gtf : All files in these directories are in GTF format
gz : All files are compacted with GNU Zip for storage efficiency.
abinitio flag为预测的基因，96为注释文件版本号，因为注释文件会不定期更新。patch为ncRNA？
Homo_sapiens.GRCh38.96.chr_patch_hapl_scaff.gff3.gz
##gff-version 3
1 havana pseudogene 11869 14409 . + . ID=gene:ENSG00000223972;Name=DDX11L1;biotype=transcribed_unprocessed_pseudogene;description=DEAD/H-box helicase 11 like 1 [Source:HGNC Symbol%3BAcc:HGNC:37102];gene_id=ENSG00000223972;logic_name=havana;version=5
1 havana lnc_RNA 11869 14409 . + . ID=transcript:ENST00000456328;Parent=gene:ENSG00000223972;Name=DDX11L1-202;biotype=processed_transcript;tag=basic;transcript_id=ENST00000456328;transcript_support_level=1;version=2
1 havana exon 11869 12227 . + . Parent=transcript:ENST00000456328;Name=ENSE00002234944;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002234944;rank=1;version=1
1 havana exon 12613 12721 . + . Parent=transcript:ENST00000456328;Name=ENSE00003582793;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003582793;rank=2;version=1
1 havana exon 13221 14409 . + . Parent=transcript:ENST00000456328;Name=ENSE00002312635;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00002312635;rank=3;version=1
1 havana pseudogenic_transcript 12010 13670 . + . ID=transcript:ENST00000450305;Parent=gene:ENSG00000223972;Name=DDX11L1-201;biotype=transcribed_unprocessed_pseudogene;tag=basic;transcript_id=ENST00000450305;transcript_support_level=NA;version=2
1 havana exon 12010 12057 . + . Parent=transcript:ENST00000450305;Name=ENSE00001948541;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001948541;rank=1;version=1
1 havana exon 12179 12227 . + . Parent=transcript:ENST00000450305;Name=ENSE00001671638;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001671638;rank=2;version=2
1 havana exon 12613 12697 . + . Parent=transcript:ENST00000450305;Name=ENSE00001758273;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001758273;rank=3;version=2
1 havana exon 12975 13052 . + . Parent=transcript:ENST00000450305;Name=ENSE00001799933;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001799933;rank=4;version=2
1 havana exon 13221 13374 . + . Parent=transcript:ENST00000450305;Name=ENSE00001746346;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001746346;rank=5;version=2
1 havana exon 13453 13670 . + . Parent=transcript:ENST00000450305;Name=ENSE00001863096;constitutive=0;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00001863096;rank=6;version=1
###
Homo_sapiens.GRCh38.96.gtf.gz
#!genome-build GRCh38.p12
#!genome-version GRCh38
#!genome-date 2013-12
#!genome-build-accession NCBI:GCA_000001405.27
#!genebuild-last-updated 2018-11
1 havana gene 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
1 havana transcript 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
1 havana exon 11869 12227 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 12613 12721 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 13221 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana transcript 12010 13670 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
1 havana exon 12010 12057 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
1 havana exon 12179 12227 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
1 havana exon 12613 12697 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
1 havana exon 12975 13052 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
Homo_sapiens.GRCh38.p7.86.chr.gtf.gz
#!genome-build GRCh38.p7
#!genome-version GRCh38
#!genome-date 2013-12
#!genome-build-accession NCBI:GCA_000001405.22
#!genebuild-last-updated 2016-06
1 havana gene 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2";
1 havana transcript 11869 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 11869 12227 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 12613 12721 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana exon 13221 14409 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTHUMT00000362751"; havana_transcript_version "1"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
1 havana transcript 12010 13670 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; havana_transcript "OTTHUMT00000002844"; havana_transcript_version "2"; tag "basic"; transcript_support_level "NA";
1 havana exon 12010 12057 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; havana_transcript "OTTHUMT00000002844"; havana_transcript_version "2"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
1 havana exon 12179 12227 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; havana_transcript "OTTHUMT00000002844"; havana_transcript_version "2"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
1 havana exon 12613 12697 . + . gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; havana_gene "OTTHUMG00000000961"; havana_gene_version "2"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; havana_transcript "OTTHUMT00000002844"; havana_transcript_version "2"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
3 不同比对软件索引文件下载
Hisat2：
http://ccb.jhu.edu/software/hisat2/faq.shtml
Bowtie2：
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.bowtie_index.tar.gz
Bowtie
http://bowtie-bio.sourceforge.net/index.shtml
wget ftp://ftp.ccb.jhu.edu/pub/data/bowtie_indexes/GRCh38_no_alt.zip