Table 2.

Features of CSI NGS Portal.

	Full-automation	All the pipelines run from input to output without intervention with minimal user input.
	Usability	User-friendly and simple design with interactive tables having search, filter, sort, edit, export and share options.
	Modularity	Repertoire of pipelines is easy to expand complying with the existing website framework.
	Flexibility	Pipelines written in virtually any script language can be integrated independently of the website code.
	Transparency	The pipelines documentation are available online with the descriptions and the code.
	Responsive design	The website can be functionally displayed on multiple devices and platforms with different window/screen sizes.
	Quality control	FastQC report is auto-generated upon file upload, sequence and quality trimming are optionally available with multiple options.
	User privacy	No personal information is collected, secure, random cookies for authorisation and dynamic usernames for data sharing are used.
	Data privacy	Data can be edited, deleted or shared only by the owner, expired data are completely removed from the server.
	Data sharing	Uploaded raw FASTQ files are private to the user, results can be optionally shared/unshared with other users any time.
	Data availability	Data is fully accessible via the portal until expiry (10 days, subject to revision upon usage and server capacity).
	Data download	All the data can be downloaded to local computer with a few clicks via browser and command line.
	IGV-integrated	Alignment (.bam, .bigwig) and mutation (.vcf) data can be viewed in local IGV without downloading the original files.
	UCSC-integrated	Peak regions (.bigbed, .bigwig) and sites from supported pipelines can be viewed in UCSC Genome Browser online as a track hub.
	Real-time logging	Real-time overall job progress log and individual tool log files are generated useful for tracking and debugging.
	E-mail notification	User is notified upon job completion if e-mail address is provided during job submission (optional).
	Parallelisation	Jobs are parallelised by multi-threading and by simultaneous run of multiple samples wherever possible.
	New pipelines	Popular and established bioinformatics pipelines for new data types are continuously added.
	Up-to-date	All the tools and packages are regularly updated to the latest stable versions available.

Icons are made by Freepik and obtained from www.flaticon.com.