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2021 AFC General Discussion

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Prefetch is a part of the SRA toolkit. This program downloads Runs (sequence files in the compressed SRA format) and all additional data necessary to convert the Run from the SRA format to a more commonly used format. Prefetch can be used to correct and finish an incomplete Run download.

You can also avoid the prefetch step and download and convert the Run in one step by entering just the Run accession without the .sra extension in your fasterq-dump or sam-dump command:

The --type command allows you to specify the type of file to download. You can look up the file type of the original files in either SRA in BigQuery or the Data Access tab on the Run Browser or use any to get all available formats.

To download metadata for each Run in your Entrez query click Send to on the top of the page, check the File radiobutton, and select RunInfo in pull-down menu.

The genome download service in the Assembly resource makes it easy to download data for multiple genomes without having to write scripts. To use the download service, run a search in Assembly, use facets to refine the set of genome assemblies of interest, open the "Download Assemblies" menu, choose the source database (GenBank or RefSeq), choose the file type, then click the Download button to start the download. An archive file will be saved to your computer that can be expanded into a folder containing the genome data files from your selections.

The genome download service is best for small to moderately sized data sets. Selecting very large numbers of genome assemblies may result in a download that takes a very long time (depending on the speed of your internet connection). Scripting using rsync is the recommended protocol to use for downloading very large data sets (see below).

We recommend using the rsync file transfer program from a Unix command line to download large data files because it is much more efficient than older protocols. The next best options for downloading multiple files are to use the HTTPS protocol, or the even older FTP protocol, using a command line tool such as wget or curl. Web browsers are very convenient options for downloading single files even though they will use the FTP protocol because of how our URLs are constructed. Other FTP clients are also widely available but do not all correctly handle the symbolic links used widely on the genomes FTP site (see below).

Replace the "ftp:" at the beginning of the FTP path with "rsync:". E.g. If the FTP path is _001696305.1_UCN72.1, then the directory and its contents could be downloaded using the following rsync command:

Replace the "ftp:" at the beginning of the FTP path with "https:". Also append a '/' to the path if it is a directory. E.g. If the FTP path is _001696305.1_UCN72.1, then the directory and its contents could be downloaded using the following wget command:

NCBI redesigned the genomes FTP site to expand the content and facilitate data access through an organized predictable directory hierarchy with consistent file names and formats. The site now provides greater support for downloading assembled genome sequences and/or corresponding annotation data with more uniformity across species. The current FTP site structure provides a single entry point to access content representing either GenBank or RefSeq data.

Files for old versions of assemblies will not usually be updated, consequently, most users will want to download data only for the latest version of each assembly. For more information, see "How can I download only the current version of each assembly?".

For some assemblies, both GenBank and RefSeq content may be available. RefSeq genomes are a copy of the submitted GenBank assembly. In some cases the assemblies are not completely identical as RefSeq has chosen to add a non-nuclear organelle unit to the assembly or to drop very small contigs or reported contaminants. Equivalent RefSeq and GenBank assemblies, whether or not they are identical, and RefSeq to GenBank sequence ID mapping, can be found in the assembly report files available on the FTP site or by download from the Assembly resource.

Tab-delimited text file reporting hash values for different aspects of the annotation data. The hashes are useful to monitor for when annotation has changed in a way that is significant for a particular use case and warrants downloading the updated records.

Genome Workbench project file for visualization and search of differences between the current and previous annotation releases. The NCBI Genome Workbench web site provides help on downloading and using the 64-bit version of Genome Workbench.

Only FTP files for the "latest" version of an assembly are updated when annotation is updated, new file formats are added or improvements to existing formats are released. Consequently, most users will want to download data only for the latest version of each assembly. You can select data from only the latest assemblies in several ways:

Variants of these instructions can be used to download all draft bacterial genomes in RefSeq (assembly_level is not "Complete Genome"), all RefSeq reference or representative bacterial genomes (refseq_category (column 5) is "reference genome" or "representative genome"), etc.

I have to pull this list of customers in existing customer table. if this customer already exists then do nothing if this customer is not in list then add in Customer table. I need some guidance if this could be done through SSIS, if yes then how? I have no idea how to implement this in SSIS. I was trying to write a win32 service in c# to download text file locally and then run BCP to export data in a temp file then call SP to see if the customer is updated then update else if not found then add in Customer table. I am not sure if this could be done through SSIS and if yes i hope it would be fast and quick to implement, if someone already worked on it. What is the best option to choose, I need to know what is the best solution and how it could be done if possible in SSIS? I need to do this on daily bases to get text file up to date with my Customer table.

You can still follow the link, istall wget and test it interactively, without SSIS to download a file from the web. Then you can use a simple batch file .bat to test the download in batch mode. when this works, then run this batch file in SSIS by using Execute Process Task, read more on this link

Thanks for help. I got success to download file locally using script task, but when I try to import this text file data through BULK insert script or through Import/Export wizard, I am facing following error:

I have attached two files the sample.txt is one that is imported/downloaded through SSIS. which is giving above error - this is because the line terminator seems missing, however if i go to site and copy and paste the text which you can see in sample1.txt, the BULK statement successfully import data in SQL Server table. I used following script to import:

If you are not comfortable with BCP format files, then pre-treat the file itself converting the UNIX format to Windows format. Google UNIX2DOS utility for Windows and there are free downloads for this utility.

--ignore-glacier-warnings (boolean)Turns off glacier warnings. Warnings about an operation that cannot be performed because it involves copying, downloading, or moving a glacier object will no longer be printed to standard error and will no longer cause the return code of the command to be 2.

--request-payer (string)Confirms that the requester knows that they will be charged for the request. Bucket owners need not specify this parameter in their requests. Documentation on downloading objects from requester pays buckets can be found at

In addition to searching OMIM through the website, OMIM offers a number of data files that are updated nightly and are available for download following a registration and review process. Registration is necessary to keep a record of downloads for funding purposes* and to notify users of changes and updates. One file, mim2gene.txt, is provided without registration to help interconnectivity of MIM numbers among other data resources.

Please ensure that you describe accurately how you plan to use OMIM so that we can process your registration quickly. Once your registration is approved you will receive an email containing a set of urls which will allow you to download the data. Non-compliant registrations will be automatically rejected.

Please read this USE AGREEMENT carefully before using this website. This Use Agreement applies to any individual, institution, or organization that uses through its front end, including its mirror sites, the API, or downloads of OMIM data from the site.

Use of is provided free of charge to any individual for personal use, for educational or scholarly use, or for research purposes through the front end of the database. Any individual , commercial and not-for-profit entities and institutions (hereafter called User) wishing to download all or part of OMIM is subject to the terms of this USE AGREEMENT.

Users at for-profit or commercial entities who want to download all or part of OMIM must obtain a license by paying applicable licensing fees to and entering into a license agreement with JHU which has the exclusive right to license the access to and use of OMIM to users worldwide. Such license agreement may be in standard form or negotiated between you and JHU. By accessing and using OMIM or related information, you agree to be bound by our standard license agreement and pay any related fees stipulated therein. In addition, if you access OMIM without a license, you agree to payment of penalties of double the standard license. Requests for information regarding a license for commercial use of the OMIM database may be sent via e-mail to 041b061a72


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