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NextGen Workbench
The way the bioinformatics should be...
Lister row height
Change Lister row height.
The Lister shows all sequences in your SFF/FastQ file, their average quality, bases, comments, quality graph, sequence length
Default = 15 pixels
Disk buffer size
Default= 320KB
Increasing this size will not necessary increase the performance of the program.
You will have to experiment to find the best value for your computer.
Experiment first with extreme values (16KB to 640KB) then find the average point between these extremes.
Note: SSD disks may perform better with slightly larger values.
Maximum FastQ record length
Enter here the maximum FastQ record length that you expect to ever find.
Smaller values results in minor performance improvement! However, if the program encounters a sequence longer than this value, it will probably crash.
In this case, simply enter a higher value.
This value is calculated like this:
Value = B*2+ C*2
Where:
- B is maximum number of bases you ever expect to find
- C is comment length
Example:
For a FastQ file where the longest read ever is 300 bases and the comment 100 chars, the value is 800. Choose 900, 'just in case'.
The table below shows which is the MAXIMUM size you should expect for your reads, based on the technology used:
Technology |
Read length (average) |
Read length (maximum) |
Reads/run |
Size/run |
Advantages |
PacBio RS II (single molecule real time sequencing) |
4 000 |
20 000 |
60 000 |
1 600 Mb |
Quantitative, no amplification |
Roche GS FLX+ (454) |
700 |
1 000 |
1 000 000 |
700 Mb |
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Illumina HiSeq 2500 |
2 x 100 |
2 x 125 |
6 billions |
600 Gb |
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Illumina MiSeq |
50 - 300 |
? |
50 000 000 |
15 Gb |
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Safe value:
If you don't know how long your sequences could be use the maximum value which is 40200 or check the user manual for details.
Loading files directly from Win Explorer (Associate with...)
Associating NextGen Workbench with SFF/FastQ files will allow you to open SFF/FastQ files directly from Windows Explorer when you double click them.
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