參考：http://blog.csdn.net/Cs_mary/article/details/78378552 ###prefetch 參數解釋
https://www.ncbi.nlm.nih.gov/books/NBK158900/#SRA_download.how_do_i_use_the_sra_toolki ## convert data into a particular format (fastq-dump等）
https://github.com/ncbi/sra-tools/wiki/Downloads ###sra-tools軟件的下載，不同系統（Centos ubuntu window）
http://blog.csdn.net/xubo245/article/details/50513201 ###用Aspera connect從NCBI上下載SRA格式數據
https://indexofire.gitbooks.io/notebook_of_analyzing_pathogen_ngs_data/content/chapter_1/sra.html
http://boyun.sh.cn/bio/?p=1933
一. window
1.下載地址：
http://downloads.asperasoft.com/connect2/
2.下載：
數據下載地址：
http://www.ncbi.nlm.nih.gov/projects/faspftp/1000genomes/
其他地址：
http://www.1000genomes.org/aspera
二 linux
1、下載安裝
http://downloads.asperasoft.com/
curl -O http://download.asperasoft.com/download/sw/connect/3.6.1/aspera-connect-3.6.1.110647-linux-64.tar.gz
tar zxf asper-commect-3.6.1.110647-linux.tar.gz
sh aspera-connect-2.4.7.37118-linux-64.sh
2、##加入路徑
echo "alias acsp=/home/sxuan/.aspera/connect/bin/ascp" >> ~/.bashrc
3、下載地址查找：http://www.ncbi.nlm.nih.gov/Traces/study/
1）單個下載：ascp -i /your-path-to/.aspera/connect/etc/asperaweb_id_dsa.openssh anonftp@ftp-private.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR689/SRR689250/SRR689250.sra ./
2）批量下載：整理成下面的格式黏貼在文本SRR_Download_List_file_list.txt 中：
/sra/sra-instant/reads/ByRun/sra/SRR/SRR689/SRR689250/SRR689250.sra
/sra/sra-instant/reads/ByRun/sra/SRR/SRR893/SRR893046/SRR893046.sra
nohup ascp -i /share/home/jialj/.aspera/connect/etc/asperaweb_id_dsa.putty --mode recv --host ftp-private.ncbi.nlm.nih.gov --user anonftp --file-list SRR_Download_List_file_list.txt ./ &
三 prefetch直接調用ascp，沒有安裝ascp之前直接用http
-f | –force Force object download. One of: no, yes, all. no [default]: Skip download if the object if found and complete; yes: Download it even if it is found and is complete; all: Ignore lock files (stale locks or if it is currently being downloaded: use at your own risk!).
強制下載
默認：文件已經存在則跳過
yes: 即使已存在完整文件仍然下載
–transport Value one of: ascp (only), http (only), both (first try ascp, fallback to http). Default: both.
傳輸
默認： 先嘗試ascp, 再嘗試http
-l | –list List the contents of a kart file.
列表kart文件
-s | –list-sizes List the content of kart file with target file sizes.
列表Kart文件及文件大小
-N | –min-size Minimum file size to download in KB (inclusive).
最小下載文件大小
-X | –max-size Maximum file size to download in KB (exclusive). Default: 20G.
最大下載文件大小
默認 20G
-o | –order Kart prefetch order. One of: kart (in kart order), size (by file size: smallest first). default: size.
Kart文件下載順序
默認：按文件大小順序下載
-a | –ascp-path
prefetch -a “/opt/aspera/bin/ascp|/opt/aspera/etc/asperaweb_id_dsa.openssh” SRR390728
When the toolkit is unable to locate an installed version of Aspera, the location of ascp and ssh key (-a /opt/aspera/bin/ascp|/opt/aspera/bin/asperaweb_id_dsa.openssh”) can be provided.
無法自動調用Aspera時就需要提供ascp的路徑和密鑰
prefetch -t ascp -a “/opt/aspera/bin/ascp|/opt/aspera/bin/asperaweb_id_dsa.openssh” --list SRR.file
prefetch -c SRR390728
This command will check the availability of all needed reference sequences (-c) for a given accession.
檢查給定序列號是否可以能夠下載
=====================================
批量下載SRRxxxxxx
# 如何下載多個文件？創建一個含有SRR runs的文件。
echo SRR1553608 > sra.ids
echo SRR1553605 >> sra.ids
# 用這個文件去prefetch對應的runs.
prefetch --option-file sra.ids
# 拆包下載好的所有文件。請注意下邊的做法不是特別妥當，因為（文件夾里）除了我們用sra.ids下載的，可能還有別的prefetch下來的文件。
fastq-dump --split-files ~/ncbi/public/sra/SRR15536*
--split-files: By using this, one single SRR file will download as SRRxxx_1.fastq and SRRxxx_2.fastq.
--split-3: which splits your SRR into 3 files: one for read 1, one for read 2, and one for any orphan reads (ie: reads that aren’t present in both files). This is important for downstream analysis, as some aligners require your paired reads to be in sync (ie: present in each file at the same line number) and orphan reads can throw this order off.