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An efficient SFF/FastQ viewer and editor (GUI)

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  • An efficient SFF/FastQ viewer and editor (GUI)

    I was in need for a FastQ editor that is fast, has a GUI and works also on Windows. Also PREFERABLY without dependencies like Java/DotNet. After some quite long search I couldn't find one so I decided to build my own. I am a biologist but I have some programming skills also.

    Until now I have a full SFF/FastQ viewer with some editing options also:
    * Detect low quality (untrusted) ends
    * Clip untrusted ends
    * Trim poly-A/T tails with minimum length of x bases
    * Cut reads shorter than x bases
    * Cut reads longer than x bases
    * Cut reads with average QV under specified threshold
    * Cut reads if they contain N bases (I can specify how many)
    * Cut read if x% of bases are either A, C, T or G
    * Split multiplexed files (barcode detection via perfect match or assembly)
    * Read lister - Show all reads (no matter how many they are). It can show: Read name, Base sequence, average quality, sequence length
    * 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


    The memory footprint for opening any file (no matter how large) should never exceed 30MB.
    The program is free of course.

    Feedback will be highly appreciated.
    Last edited by create.share; 06-03-2014, 01:25 AM. Reason: screenshot

  • #2
    There has been an update today:

    Release history

    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 (colapsed/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 scrollbar 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 cmdline (needed for 'Associate with...')


    Download
    Last edited by create.share; 06-03-2014, 01:15 AM.

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    • #3
      Hola create.share.
      I am trying ti use your program to extract the fastq file from the sff. I am able to see some quality parameter if i click the sample but I don't really know how to extract. I am working with a big amount of datas, 350 samples...and I am not sure if i could do that using your program. My intention would be to extract the fastq file in order to have a look using fastQC program.
      Could you help me with that?

      Thanks in advanced,
      Elisa

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      • #4
        Hmmm...download links don't seem to work for Mac or Linux...

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        • #5
          I am working on windows jpummil. Have you tried this tool before?

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          • #6
            Originally posted by elizondas View Post
            I am working on windows jpummil. Have you tried this tool before?
            No, I just happened on the announcement here on SEQanswers and wanted to share it with my Bio community here at the University of Arkansas...but...most of the users are on Macs, and I am manager of HPC for a large Linux cluster (and use Linux on all of my laptops, workstations, etc), thus the confusion when I saw the download links for the various platforms on the main page

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            • #7
              ah, sorry. You could try to contact with them trough the webpage...

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              • #8
                Version 2.0 will be released soon. After that the program will be ported to Mac and then to Linux. Just hang on a bit... Until then you can send feedback. I hope it is useful to the bioinf community.

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                • #9
                  The third version is out: NextGen Workbench 3
                  Now it integrates with CD Hit Sequence Dereplicator

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                  • #10
                    I'm trying (on Windows 7) to use Next Workbench 3's SFF editor on some 454 sff files, but when I do end clipping and filtering, none of it is saved and the sequence itself never changes even after 'apply and save'.

                    examples:
                    -- told it to clip the first 4 nt off the 5' end--> apply and save --> no change in either preview sequence or saved sequence
                    -- told it to apply the sff file's own clipping and filtering settings -->no changes in either preview or saved sequence



                    I *am* able to convert from sff --> fastq using this tool, but that's about all so far (and even then quality profiles of the fastq files look strangely different from the sffs).
                    Last edited by ssully; 11-07-2014, 11:13 AM.

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                    • #11
                      Which version are you using? v3.1 is the latest one. It works here.
                      Last edited by motan; 05-18-2015, 03:22 AM.

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                      • #12
                        Originally posted by ssully View Post
                        I *am* able to convert from sff --> fastq using this tool, but that's about all so far (and even then quality profiles of the fastq files look strangely different from the sffs).
                        Can you send a bug report over email?
                        1. Version that you are using
                        2. Description of the problem (maybe with screenshots)
                        3. If possible a small (SFF) file that shows the problem. This will definitively speed up the clarification of the problem.

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