NextGen Workbench

The way the bioinformatics should be...

Processing SFF/FastQ files

The information coming form the sequencing machine is far from ready-to-use. It may contain: duplicate samples adaptor sequences too short reads too long reads reads with low quality ends that need to be clipped NextGen Workbench will help you to clean your SFF/FastQ. The following filters can be applied: Trim poly-A/T tails Cut reads with average QV under specified threshold Cut reads if they contain N bases (the user can specify how many) Cut reads longer than x bases Cut low complexity reads Trim low quality ends. Automatically detect and cut low quality bases at the end of each read. Three parameters are used by this function. Cut reads shorter than x bases.

'Clip low quality ends' filter

Clipping information is already present in SFF files. However, in many cases the biologist may not be happy with this clipping information (the sequencing company may have been to lenient). Therefore, the user may want to cut deeper into the sequences.

You should definitively apply this filter on your FastQ files since FastQ does not contain clipping info.

To apply your custom clipping filter click the 'Custom quality clipping algorithm' and the 'Settings'. This will open the following dialog box:

This filter is applied on all reads in your FastQ/SFF file.

Applying the filters

Press the 'Refresh graphs' button to immediately see the effect of the applied filters. The effect will be seen in the Graphics panel.

Saving the filtered file

When you are happy with the results you can proceed saving the file to disk by pressing the 'Refresh and save...' button. The file will be saved in the format choused in the 'Output format' panel.