-
Notifications
You must be signed in to change notification settings - Fork 29
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Update the readme, mention alternative packages.
- Loading branch information
Showing
1 changed file
with
17 additions
and
10 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,17 +1,24 @@ | ||
# SRA-Explorer | ||
|
||
Mini web application to explore the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra) | ||
and easily access downloads for data, either as `.sra` files from the NCBI | ||
or as `.fastq` via the [EBI ENA](https://www.ebi.ac.uk/ena). | ||
Mini web application to explore the [NCBI Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra) and easily access downloads for data, either as `.sra` files from the NCBI or as `.fastq` via the [EBI ENA](https://www.ebi.ac.uk/ena). | ||
|
||
This tool has the benefit of working out of the box, entirely in your browser | ||
with no need for any back-end setup. You can use it in two ways: | ||
This tool should out of the box, entirely in your browser with no need for any back-end setup. You can use it in two ways: | ||
|
||
1. Directly on the web: http://sra-explorer.info/ | ||
2. Download the `index.html` file and load in your web browser. | ||
|
||
All the code relating to the SRA API calls are taken from | ||
[Labrador](https://github.com/ewels/labrador). The page is built using | ||
the [Bootstrap](http://getbootstrap.com) CSS framework and all of the interaction | ||
magic happens using [AngularJS](https://angularjs.org). The copy to clipboard | ||
buttons are powered by [Clipboard.js](https://clipboardjs.com/). | ||
SRA-Explorer was a fun mini-project done in my spare time. If you have found it useful, why not [tag me in a tweet](https://twitter.com/tallphil) 😁 | ||
|
||
## Packages used | ||
|
||
All the code relating to the SRA API calls are taken from [Labrador](https://github.com/ewels/labrador). The page is built using the [Bootstrap](http://getbootstrap.com) CSS framework and all of the interaction magic happens using [AngularJS](https://angularjs.org). The copy to clipboard buttons are powered by [Clipboard.js](https://clipboardjs.com/). | ||
|
||
## Alternatives | ||
|
||
If you're here a lot, it may be worth taking a look at some excellent command-line alternatives. For example: | ||
|
||
* [nf-core/fetchngs](https://nf-co.re/fetchngs) | ||
* [pysradb](https://github.com/saketkc/pysradb) | ||
* [fetchfastq](https://github.com/pachterlab/ffq) | ||
|
||
These tools are more scalable and stable than SRA-Explorer. |