NextGen Workbench

A graphic FastQ/SFF viewer & editor

The way the bioinformatics should be...

• Working with SFF/FastQ files
  • Input files
    • SFF
    • FastQ/FQ
    • Encoding
  • Output file format
• Converting SFF/FastQ files
  • Convert SFF to FastQ
  • Convert SFF to Fasta
  • Convert FastQ to Fasta (multiFasta)
• Processing SFF/FastQ files
  • 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.
  • Saving the filtered file to disk

Tools and converters

• File splitter
• Compact FastQ files
• Dereplicate sequences (under development)
• Convert FastQ file to a different encoding (under development)
• MID/Barcode splitter (split multiplexed files) (under development)
• How to merge FastQ files?
• How to split/convert multiFasta/SFF/FastQ files to Fasta?

Graphs and data analysis

• Read lister
  • Graphic quality representation for each individual read. Color coded.
• Sequence length distribution graph
• Per base sequence quality graph
• Per base GC content graph
• Per base sequence content graph
• Per base N content graph (integrated in the 'Per Base Content' graph)
• Per sequence quality scores graph graph
  • Graphs can be expanded to full screen
  • All graphs are update in real time as the file is processed
• File statistics

GUI / System

• Open SFF/FastQ files when user double clicks them in Windows Explorer
• Open file passed via command line
• Save/remember GUI state
• Easy to use file browser (allows you to quickly locate your FastQ/SFF files)
• Long operations can be easily canceled
• Fully configurable

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