写在前面

CJchen 很早之前就描述了如何 批量下载JGI（phytozome植物基因组数据库）数据。我这里只进行一个简单介绍。

介绍

JGI | Phytozome: https://phytozome-next.jgi.doe.gov/

JGI | Phytozome - 图1

下载数据

搜索想要下载的物种基因组数据，将其添加到购物车。随后在购物车获取命令行下载。

JGI | Phytozome - 图2

  1. curl --cookie jgi_session=/api/sessions/c5d3cedc7361ff1439f0e7e954c273aa --output download.20241210.102316.zip -d "{\"ids\":{\"Phytozome-533\":[\"5d94dc9fc0d65a87debccfd3\",\"5d94dc9ec0d65a87debccfc8\",\"5d94dc9fc0d65a87debccfcd\",\"5d94dc9fc0d65a87debccfd7\"]}}" -H "Content-Type: application/json" https://files-download.jgi.doe.gov/filedownload/
  3. unzip download.20241210.102316.zip
  4. ## Archive:  download.20241210.102316.zip
  5. ##   inflating: Download_876507_File_Manifest.csv  
  6. ##  extracting: Phytozome/PhytozomeV13/Ptrichocarpa/v4.1/annotation/Ptrichocarpa_533_v4.1.gene.gff3.gz  
  7. ##  extracting: Phytozome/PhytozomeV13/Ptrichocarpa/v4.1/annotation/Ptrichocarpa_533_v4.1.protein.fa.gz  
  8. ##  extracting: Phytozome/PhytozomeV13/Ptrichocarpa/v4.1/annotation/Ptrichocarpa_533_v4.1.cds.fa.gz  
  9. ##  extracting: Phytozome/PhytozomeV13/Ptrichocarpa/v4.1/assembly/Ptrichocarpa_533_v4.0.fa.gz

数据整理

mv Phytozome/PhytozomeV13/Ptrichocarpa/v4.1/assembly/Ptrichocarpa_533_v4.0.fa.gz Populus_trichocarpa.genome.fa.gz

mv Phytozome/PhytozomeV13/Ptrichocarpa/v4.1/annotation/* .
mv Ptrichocarpa_533_v4.1.cds.fa.gz Populus_trichocarpa.cds.fa.gz
mv Ptrichocarpa_533_v4.1.gene.gff3.gz Populus_trichocarpa.gff.gz
mv Ptrichocarpa_533_v4.1.protein.fa.gz Populus_trichocarpa.pep.fa.gz

gunzip *gz

rm -r Phytozome download.20241210.102316.zip Download_876507_File_Manifest.csv

exa --tree .
## .
## ├── Populus_trichocarpa.cds.fa
## ├── Populus_trichocarpa.genome.fa
## ├── Populus_trichocarpa.genome.fa.fai
## ├── Populus_trichocarpa.gff
## ├── Populus_trichocarpa.pep.fa
## └── run.sh

参考

https://jgi.doe.gov/

JGI: https://genome.jgi.doe.gov/

JGI | GOLD: https://gold.jgi.doe.gov/

JGI | Phytozome: https://phytozome-next.jgi.doe.gov/