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Hi everyone. I'm working on a small fish genome and want to know if anyone is having any success using the new fast flow cells for HiSeq that give >100bp reads as input along with a 3000bp mate pair read as the input for allpaths rather than making the 180bp library. The fast flow cells generate single reads rather than paired reads which is why I'm not sure if this will work. Any input is appreciated especially if you have tried this.
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That is not correct. Rapid mode flowcells can generated paired-end reads.Originally posted by troendle View Post -
Yes they can produce paired end reads but the library that we are attempting to work from is a 450bp library so they would not be overlapping. What we want to know is if allpaths can handle non-paired reads, or if we need to go ahead and make the 180bp library.Comment
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Ok. Your original post was not clear.
You may want to consider running on MiSeq with the new v.3 kits. That can give you 2 x 300 bp reads.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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