General tips about composing a command using the CLC Command Line Tools
Go Back Information about how to compose and run QIAGEN CLC Command Line Tools (CLT) commands is covered in the manual, which you can find in HTML or PDF format: https://resources.qiagenbioinformatics.com/manuals/clcservercommandlinetools/current/index.php?manual=Introduction.html In terms of building up your own commands when starting out, one approach would be to
How to access the usage information for the QIAGEN CLC Command Line Tools is covered in the manual starting here: https://resources.qiagenbioinformatics.com/manuals/clcservercommandlinetools/current/index.php?manual=Basic_usage.html In brief, if you submit a command of the following form: clcserver -U <username> -W <password or passcode> -S <serverhost> and your credentials were fine, the top level commands that can be run on your CLT should be printed on the screen. That is, the commands options that could be provided as arguments to the -A option, as well other major options (-C, -D, -G and so on). Let us give an example with De novo assembly command. The information returned above would let you know that the relevant option to use after the -A flag would be denovo_assembly At that point, the command to find out more about how to set up the details of the de novo assembly could be determined by running a command of this form:
This would return the command line options relevant to de novo assembly.
In terms of data input for tools like de novo assembly, where you may have multiple input data objects containing sequence reads, you would enter your each sequence list (sets of reads) after its own The above is just a short summary of tips for getting started. We highly recommend referring to the manual and explore the commands and their options, if you plan to use the CLT for your own analyses. |