sratoolkitのインストールと簡単な使用
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インストール環境
インストール環境
Ubuntu18.10 sratoolkit2.9.2-ubuntu64
インストールプロセス
1、からhttps://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/のNCBI SRA Toolkit latest release compiled binaries and md 5 checksumsダウンロードインストールパッケージ.2、パッケージを取り付けるsudo mv sratoolkit.current-ubuntu64.tar.gz -t /optそしてcd /opt
tar xzvf sratoolkit.current-ubuntu64.tar.gz
echo "export PATH=\$PATH:/opt/sratoolkit.2.9.2-ubuntu64/bin" >> ~/.bashrc
source ~/.bashrc
fastq-dump -h
ここでインストールが完了しました.
単純な使用
1、コマンドprefetchはリモートサイトからファイルをダウンロードできるprefetch SRR15536102、sraをfastqに変換する:fastq-dump SRR15536103、sraをfastaに変換する:fastq-dump --fasta 50 SRR15536104、両端シーケンシングファイルを分ける:fastq-dump --split-files SRR1553610What is the purpose of the SRA toolkit?
The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format to the following formats:
ABI SOLiD native (colorspace fasta/qual)
fasta
fastq
sff
sam (human-readable bam, aligned or unaligned)
Illumina native
You can also use the toolkit to convert from the formats listed below into the SRA format (not required for submission, but will allow you to use the SRA Toolkit to archive or analyze your data):
fastq or fasta/qual pairs
AB SOLiD-SRF
AB SOLiD-native
Illumina SRF
Illumina native
sff
Aligned bam
The SRA toolkit is available in versions compatible with Linux, Windows and Mac operating systems.
How do I use the SRA Toolkit to convert data into a particular format?
The SRA Toolkit contains a series of independent data-“dump” utilities that will allow you to convert SRA data into different file formats. As of version 2.3.2, the list of “dumpers” that are included with the toolkit include:
fastq-dump: Converts data to fastq and fasta format.
sam-dump: Converts data to sam (human-readable bam). Data submitted as aligned bam are output as aligned sam, while other formats are output as unaligned sam.
sff-dump: Converts data to sff format. Note that only data submitted as sff can be converted back to this format.
abi-dump: Converts data to csfasta/csqual format. Note that data submitted in base-space can be represented in color-space, but please be aware of the advantages/disadvantages of converting between different encodings.
illumina-dump: Converts data to Illumina native and qseq formats.
vdb-dump: Exports the vdb-formatted data of the .sra file.
Each of the above links will open the current documentation/help page for the respective utility, which include frequently used options and their definitions, usage examples, and common errors messages/solutions.
https://github.com/ncbi/sra-tools https://blog.csdn.net/sunchengquan/article/details/79781366 https://blog.csdn.net/xubo245/article/details/50510026
1、からhttps://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/のNCBI SRA Toolkit latest release compiled binaries and md 5 checksumsダウンロードインストールパッケージ.2、パッケージを取り付ける
sudo mv sratoolkit.current-ubuntu64.tar.gz -t /optそしてcd /opt
tar xzvf sratoolkit.current-ubuntu64.tar.gz
echo "export PATH=\$PATH:/opt/sratoolkit.2.9.2-ubuntu64/bin" >> ~/.bashrc
source ~/.bashrc
fastq-dump -h
ここでインストールが完了しました.
単純な使用
1、コマンドprefetchはリモートサイトからファイルをダウンロードできるprefetch SRR15536102、sraをfastqに変換する:fastq-dump SRR15536103、sraをfastaに変換する:fastq-dump --fasta 50 SRR15536104、両端シーケンシングファイルを分ける:fastq-dump --split-files SRR1553610What is the purpose of the SRA toolkit?
The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format to the following formats:
ABI SOLiD native (colorspace fasta/qual)
fasta
fastq
sff
sam (human-readable bam, aligned or unaligned)
Illumina native
You can also use the toolkit to convert from the formats listed below into the SRA format (not required for submission, but will allow you to use the SRA Toolkit to archive or analyze your data):
fastq or fasta/qual pairs
AB SOLiD-SRF
AB SOLiD-native
Illumina SRF
Illumina native
sff
Aligned bam
The SRA toolkit is available in versions compatible with Linux, Windows and Mac operating systems.
How do I use the SRA Toolkit to convert data into a particular format?
The SRA Toolkit contains a series of independent data-“dump” utilities that will allow you to convert SRA data into different file formats. As of version 2.3.2, the list of “dumpers” that are included with the toolkit include:
fastq-dump: Converts data to fastq and fasta format.
sam-dump: Converts data to sam (human-readable bam). Data submitted as aligned bam are output as aligned sam, while other formats are output as unaligned sam.
sff-dump: Converts data to sff format. Note that only data submitted as sff can be converted back to this format.
abi-dump: Converts data to csfasta/csqual format. Note that data submitted in base-space can be represented in color-space, but please be aware of the advantages/disadvantages of converting between different encodings.
illumina-dump: Converts data to Illumina native and qseq formats.
vdb-dump: Exports the vdb-formatted data of the .sra file.
Each of the above links will open the current documentation/help page for the respective utility, which include frequently used options and their definitions, usage examples, and common errors messages/solutions.
https://github.com/ncbi/sra-tools https://blog.csdn.net/sunchengquan/article/details/79781366 https://blog.csdn.net/xubo245/article/details/50510026
The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format to the following formats:
ABI SOLiD native (colorspace fasta/qual)
fasta
fastq
sff
sam (human-readable bam, aligned or unaligned)
Illumina native
You can also use the toolkit to convert from the formats listed below into the SRA format (not required for submission, but will allow you to use the SRA Toolkit to archive or analyze your data):
fastq or fasta/qual pairs
AB SOLiD-SRF
AB SOLiD-native
Illumina SRF
Illumina native
sff
Aligned bam
The SRA toolkit is available in versions compatible with Linux, Windows and Mac operating systems.