This page provides a workflow/pipeline on genomic data processing when only long reads are being used for analysis. The pipeline is described as being intermediate level, as it is differentiating based on the technology/company used to sequence (Oxford Nanopore or PacBio) and on coverage depth/quality.
To effectively utilize this page, start by exploring the major steps outlined here, which include de novo assembly and alignment/mapping. These steps are thoughtfully presented to assist beginners and new learners in getting started with genomic data analysis. To further streamline your experience, we've divided the workflow based on sequencing technology and read coverage/quality. Choose the section that most closely aligns with your data, and follow the subsequent steps as a guide. For each step, we've provided an example of a program that could be employed to accomplish the task. Clicking on the associated link will direct you to the software's manual, offering detailed instructions for its usage.
Although the pipeline and programs listed here are specific to their respective sequencing technologies, it is not always necessary to choose programs that are designed specifically based on this. Some software programs currently available can process long reads from any sequencing technology/company, both effectively and efficiently.
It's important to keep in mind that while this guide serves as a valuable starting point, it is not an exhaustive resource and may need adaptation based on the specific characteristics of your data and other parameters. Genomic research is continually evolving, so remain flexible and open to adjustments as your project progresses.
In place of NanoCorr which is no longer supported, check out NanoRevisor instead.
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