◆ Unix, Windows, or Macintosh workstation with an Internet connection and web browser (Firefox, Chrome, Safari or Internet Explorer).
◆ Command-line user interface (CLI). Macs have a built-in CLI called Terminal, which is usually in Macintosh HD/Applications/Utilities/Terminal. Some users may prefer iTerm (https://www.iterm2.com/), Windows machines do not include a CLI, but there are many available for download, including: ConEmu (https://conemu.github.io/), Console2 (https://sourceforge.net/projects/console/files/), cmder, Cygwin (https://www.cygwin.com/), and PuTTY (https://www.putty.org/).
◆ Text editor. The default Mac text editor is TextEdit (Macintosh HD/Applications/TextEdit), but better functionality is found with BBEdit (https://www.barebones.com/products/bbedit/index.html) or SublimeText (https://www.sublimetext.com/). The Windows default is Notepad (C:\Windows\System32\notepad.exe), an alternative for Windows is Emacs (https://sourceforge.net/projects/emacsbinw64/).
◆ Aspera connect high-speed file transfer software: For command line version: go to http://downloads.asperasoft.com/en/downloads/8?list and chose the version for your operating system. For web-based version: download the plugin from http://downloads.asperasoft.com/connect2/.
◆ tbl2asn (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/) (only needed for TSA submission)
◆ Sequence read data in standard FASTQ format
◆ Biological information about the sequenced organism
◆ Technical information about how the sequencing library was prepared
◆ A transcriptome assembly based on the raw reads
◆ Technical information about how the transcriptome assembly was generated