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We have a eukaryotic diploid genome assembled and scaffolded using ALLPATHS-LG. In addition, we have a linkage map generated from iso-crossing individuals and performing reduced-representation (GBS) sequencing. We have evidence from the linkage map that can place and order our scaffolds, or at times nest a scaffold within a scaffold gap of a larger scaffold, but it would be a lot of work to manual review these joins and investigate mate-pair evidence across the entire genome. I was wondering if there was any existing pipelines or software programs that generate superscaffolded assemblies based off of a mix of linkage map information and mate-pair information. I have seen several papers, but their methods are either not clearly described, or are very manual in nature, but it is likely I could be missing something.
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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