参考：http://blog.csdn.net/Cs_mary/article/details/78378552 ###prefetch 参数解释
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软件的下载，不同系统（Centos ubuntu window）
http://blog.csdn.net/xubo245/article/details/50513201 ###用Aspera connect从NCBI上下载SRA格式数据
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.下载地址：
http://downloads.asperasoft.com/connect2/
2.下载：
数据下载地址：
http://www.ncbi.nlm.nih.gov/projects/faspftp/1000genomes/
其他地址：
http://www.1000genomes.org/aspera
二 linux
1、下载安装
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、##加入路径
echo "alias acsp=/home/sxuan/.aspera/connect/bin/ascp" >> ~/.bashrc 3、下载地址查找：http://www.ncbi.nlm.nih.gov/Traces/study/
1）单个下载：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）批量下载：整理成下面的格式黏贴在文本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直接调用ascp，没有安装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!).
强制下载
默认：文件已经存在则跳过
yes: 即使已存在完整文件仍然下载
–transport Value one of: ascp (only), http (only), both (first try ascp, fallback to http). Default: both.
传输
默认： 先尝试ascp, 再尝试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).
最小下载文件大小
-X | –max-size Maximum file size to download in KB (exclusive). Default: 20G.
最大下载文件大小
默认 20G
-o | –order Kart prefetch order. One of: kart (in kart order), size (by file size: smallest first). default: size.
Kart文件下载顺序
默认：按文件大小顺序下载
-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.
无法自动调用Aspera时就需要提供ascp的路径和密钥
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.
检查给定序列号是否可以能够下载
=====================================
批量下载SRRxxxxxx
# 如何下载多个文件？创建一个含有SRR runs的文件。
echo SRR1553608 > sra.ids
echo SRR1553605 >> sra.ids
# 用这个文件去prefetch对应的runs.
prefetch --option-file sra.ids
# 拆包下载好的所有文件。请注意下边的做法不是特别妥当，因为（文件夹里）除了我们用sra.ids下载的，可能还有别的prefetch下来的文件。
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.