A SFF/FastQ viewer, editor, converter. Convert FastQ files. Convert SFF files

NextGen Workbench

A graphic FastQ/SFF viewer, editor & converter

The way the bioinformatics should be...

Release history

Proposed for v3

Sequence dereplicator
Full support for Fasta files
Multithreading
Kmer Content graph

v2.0 (current)

New tool: Demultiplexing - Split based on FastQ internal info (only for Illumina files) - Load info about adaptor clipping from sequence name (comment) line
New tool: Demultiplexing - Split multiplex file based on barcode sequence(s) provided by user. Reverse complement sequences are also supported.
New tool: Demultiplexing - Split based on FastQ internal info radio box is automatically disabled if the sequence does not contain the info
New tool: File splitter: Split huge FastQ/SFF file in chunks of x reads
New tool: File splitter: Cut all sequences in the specified range
New tool: File convertor. Converts between Fasta, FastQ, SFF
New tool: Remove overrepresented sequences.
New tool: Remove contaminants. Search overrepresented sequences against a contaminant database (allow user to add/remove seq from database)
Adaptor trimming: New function: Cut x bases at 3' / 5' end
Sequence Lister: sequences are now aligned to left
Bug fix: For some graphs the x axis was shifted with 1 position
Bug fix: Sequence Lister: columns were not resizable
Show overrepresented sequences in a table. The table is automatically saved to disk for later use. The user can also import the table content to be used in the 'Remove overrepresented seq' tab
Redesigned GUI
Save report in HTML format
Improved menus and shortcuts
New option in "Clip low quality ends": "Use the adaptor clipping info of the SFF file"
Added 'Close file' button to close currently open file
Added 'expand all graphs' function
Let user hide left/right panels
Let user choose output file/folder (for all tools)
Let user change the 'duplication level' parameters (in order to trade performance for speed)
The "Generate compact FastQ file" switch is now global (applies to all FastQ files generated by this program)
When I save a file as Fasta put read's name in the 'Comments'
SFF: show manifest info for SFF files
Show progress (in %) also in Tools
Improved compatibility with small screen laptops (768pix resolution)
Improvements in graphs: improved legend, meaning of the x axis is show right under it, etc
Duplication level chart: show on x axis the numbers as >1K, >2K, etc
Speed improvements
Link to Questionnaire in 'About' box
Web tutorial: How to convert SFF to FastQ

v1.9

Added new report: Sequence duplication level
Added new report: Overrepresented sequences
The user can set the overrepresented sequence threshold. Default is 0.1%
The overrepresented sequence table can be sorted
Fixed: (some) graphs shifted with 1
Few bugs fixed
Tested with 12GB files

v1.7 - This version brings tremendous speed improvements

Massive SFF/FastQ parsing speed optimization using buffered files
Important speed optimization when using the 'Refresh button'
The program is a bit more responsive when processing large files
Silently cut samples that have 0 good bases
Cut reads with GC under 15% or over 85%
'About' tab improvements
Added 3 preset settings in 'custom quality clipping' box
Few bugs fixed
Improved manual (still a lot of work to do)

v1.5

SFF - Added SFF support (processing, statistics, etc). The user can switch between the two settings (sff file's clip info, or user defined clip info)
Tools - File splitter. Split huge FastQ/SFF file in chunks of x reads
Tools - Compact FastQ files (remove duplicate content of the + line)
Tools - Convert SFF to FastQ
Tools - Convert SFF to Fasta
Tools - Convert FastQ to Fasta (multiFasta)
Graph - Now all graphs are updated in real time (as filters are applied)
Graph - Sequence length distribution graph
Graph - Per base sequence quality graph
Graph - Per base GC content
Graph - Per sequence GC content
Graph - Per base sequence content
Graph - Per base N content (integrated in the 'Per Base Content' graph)
Graph - Show the 'Per sequence GC content' graphs as dot instead as lines
Graph - Resize graphs automatically
Graph - Remember height of each graph panels
Graph - Remember status of each graph panel (collapsed/expanded)
Graph - Let user scroll graphs using mouse scroll
Graph - Button to expand some graphs. Support for all graphs will be added soon
Graph - Added vertical scroll bar in graph's panel so the user can make any graph as long as he wants
GUI - Fast preview. Process 1 sample every 100
GUI - Make beep when processing is done!
GUI - Let user set GUI refresh interval (for example every 10000 reads)
GUI - Allow user to cancel a long operation
GUI - Show basic statistics: file name, file size, number of reads (before and after filtering), encoding, per file GC percent
System - Start program to a certain folder via command line
System - Memory efficient parsing
System - Associate itself with FastQ files. Load file via command line (needed for 'Associate with...')

v1.2

Tools - Trim poly-A/T tails
Tools - Cut reads with average QV under specified threshold
Tools - Cut reads if they contain N bases (the user can specify how many)
Tools - Cut reads longer than x bases
Tools - Ask where to save the file (at conversion)
Tools - Cut low complexity reads
Tools - Trim low quality ends. Automatically detect and cut low quality bases at the end of each read. Three parameters are used by this function.
Tools - Cut reads shorter than x bases.
Tools - Save the filtered file to disk (use the 'Refresh graph and save...' button).
Tools - Encoding auto detection was checked and works correctly.
Lister - Let user choose row height
Lister - Show all reads (no matter how many they are). It can show: Read name, Base sequence, average quality, sequence length, mini chromatogram.
Graph - Per sequence quality scores graph
GUI - Show basic statistics: file name, number of reads (before and after filtering), encoding
GUI - Show info about encoding as soon as possible
GUI - Show processing time (in real time)
GUI - Save/remember GUI state
GUI - Remember last open tab

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