本文近期更新地址：
随着測序技术的不断提高。二代測序数据成指数增长。
NCBI提供了SRA数据库存储这些数据。
http://www.ncbi.nlm.nih.gov/sra
为了方便更好的分析这些数据，NCBI提供了下载的命令行工具：sra-toolkit。
包含下面命令：
官方文档：
http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc
prefetch: Allows command-line downloading of SRA, dbGaP, and ADSP data 下载数据
fastq-dump: Convert SRA data into fastq format # 将下载的sra数据转换为 fastq文件，支持 PE
sam-dump: Convert SRA data to sam format# sra转换为sam
sra-pileup: Generate pileup statistics on aligned SRA data
vdb-config: Display and modify VDB configuration information
vdb-decrypt: Decrypt non-SRA dbGaP data (“phenotype data”)
prefetch
经常使用命令
Data transfer:
# 假设已有下载的文件是否强制下载，默觉得非强制
-f | --force <value> 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!).
# 选择下载的方式 ascp 和 http，默认先尝试 ascp。再尝试http
--transport <value> Value one of: ascp (only), http (only), both (first try ascp, fallback to http). Default: both.
# 列举 kart 文件里的 内容，大小
# 你能够把须要下载的项目放入 kart 文件
-l | --list List the contents of a kart file.
-s | --list-sizes List the content of kart file with target file sizes.
# 设置文件的最小尺寸
-N | --min-size <size> Minimum file size to download in KB (inclusive).
# 设置文件的最大尺寸
-X | --max-size <size> Maximum file size to download in KB (exclusive). Default: 20G.
# 排序方式
-o | --order <value> Kart prefetch order. One of: kart (in kart order), size (by file size: smallest first). default: size.样例
prefetch ERR732926
直接下载 ERR732926 样本的文件，默认放入 ~//ncbi/public/sra 文件夹下
prefetch cart_0.krt
下载 kart文件里的列表
prefetch -l cart_0.krt
列举cart_0.krt文件的内容
fastq-dump
General:
-h | --help Displays ALL options, general usage, and version information.
-V | --version Display the version of the program.
Data formatting:
#切割 paired-end data
--split-files Dump each read into separate file. Files will receive suffix corresponding to read number.
--split-spot Split spots into individual reads.
# 仅仅保留fasta，没有质量得分
--fasta <[line width]> FASTA only, no qualities. Optional line wrap width (set to zero for no wrapping).
-I | --readids Append read id after spot id as ‘accession.spot.readid‘ on defline.
-F | --origfmt Defline contains only original sequence name.
-C | --dumpcs <[cskey]> Formats sequence using color space (default for SOLiD). "cskey" may be specified for translation.
-B | --dumpbase Formats sequence using base space (default for other than SOLiD).
-Q | --offset <integer> Offset to use for ASCII quality scores. Default is 33 ("!").
Filtering:
-N | --minSpotId <rowid> Minimum spot id to be dumped. Use with "X" to dump a range.
-X | --maxSpotId <rowid> Maximum spot id to be dumped. Use with "N" to dump a range.
-M | --minReadLen <len> Filter by sequence length >= <len>
--skip-technical Dump only biological reads.
--aligned Dump only aligned sequences. Aligned datasets only; see sra-stat.
--unaligned Dump only unaligned sequences. Will dump all for unaligned datasets.
# 输出数据
Workflow and piping:
-O | --outdir <path> Output directory, default is current working directory (‘.‘).
-Z | --stdout Output to stdout, all split data become joined into single stream.
--gzip Compress output using gzip.
--bzip2 Compress output using bzip2.样例
fastq-dump -X 5 -Z SRR390728
能够在不下载的情况下。显示SRR390728样本的前五个读段（20行）
fastq-dump -I –split-files SRR390728
处理 paired-end 文件
Produces two fastq files (–split-files) containing “.1” and “.2” read suffices (-I) for paired-end data.
fastq-dump –split-files –fasta 60 SRR390728
Produces two (–split-files) fasta files (–fasta) with 60 bases per line (“60” included after –fasta).
fastq-dump –split-files –aligned -Q 64 SRR390728
Produces two fastq files (–split-files) that contain only aligned reads (–aligned; Note: only for files submitted as aligned data), with a quality offset of 64 (-Q 64) Please see the documentation on vdb-dump if you wish to produce fasta/qual data.
列举出经常使用命令，假设有其它须要请阅读官方文档。