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Newbler and Celera have maximum read lengths of ~2048bp I believe. I've got a few libraries of Sanger random shear that have read lengths a little larger than that. I've also got several libs of 454 data, assembled with newbler into contigs, and several libs of Illumina, assembled with velvet and/or CLC into contigs. What's the best option to overlap all these (reasonably large) contigs into a new assembly?
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I always reach for some "standard" overlap assembler like phrap or AMOS-minimus. Although it doesn't always work as well as I'd like / expect. Interested to hear your experiences. Celera might be another option. -
Cap3 can be one possibility too. Velvet also work to long reads with "-long" parameter.Comment
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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.
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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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