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Hi,
Can anyone suggest any good visualization tools for sequence alignments and assembling?
Thanks,
Dicty
Can anyone suggest any good visualization tools for sequence alignments and assembling?
Thanks,
Dicty
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The seqanswers wiki is your friend. Examples with:
- assembly visualization
- visualization
- genome browser
There is also a huge thread somewhere about genome browsers, with tablet, igv, igb, jbrowse, etc etc.. i would use the search function of the forum (up there). -
Thanks a lot for your response. It's very helpful.Comment
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If you have a genuine assembly that you wish to *edit*, the choice is more restricted. I'll declare an interest/bias as I'm the primary author of Gap5, however I believe Consed has also received updates to allow it to edit NGS assemblies.
That said, if it's just visualisation that you need then the myriad of tools out there listed in the links above will do a fine job, and indeed many will be better than Gap5 would due to DAS source integration and proper handling of reference based coordinates.
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Thanks a lot, jkbonfield. Currently I only want to visualize the alignment and assembly results, but probably I will use Staden for further analysis.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.
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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 -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
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