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Fastq software/programs
Hello, so I have a simple question, what programs can you use to open and read FASTQ files?
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Fastq files are text. So in principal you can use a text editor to open the file (or use cat/more utilities to look at the contents).
In general you will want to do QC/Trimming/Pre-processing/Alignments using the fastq files to do secondary data analysis. -
And some of the programs for QC/Trimming/Pre-Processing/Alignments and secondary data analysis are? Thank you very much btw, it's really appreciated.Comment
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There are links for each of the programs in my post above. If you do not see them then temporarily disable "no script" or any other similar plugin that you may be using to see the links.
QC: http://www.bioinformatics.babraham.a...ojects/fastqc/
Trimming: http://www.usadellab.org/cms/?page=trimmomatic
Pre-processing: http://en.wikibooks.org/wiki/Next_Ge...Pre-processing
General Analysis: http://en.wikibooks.org/wiki/Next_Ge...cing_%28NGS%29Comment
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This is exactly what I was looking for today, thanks again!Comment
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Hi FredTam1,
You can open and read your FASTQ files in any linux based platform or Mac OS systems through the terminal.
you can use either cat filename
or
vi filename
FASTQ files are usually big sized, so you need not &/ not required to read the entire file.
Good luck ahead.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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