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Jenna M. Lang added Discussion.md
about 10 years ago
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In an effort to democratize the process of microbial sequencing and de novo assembly, we have designed a workflow that would allow a small lab, one operating without a lab technician or bioinformatician to take a sample and carry it through from swab to publication. There are many options for sequencing, assembling, and annotating microbial genomes. This workflow is only one path through the many choices that could be made in a genome sequencing project. A large lab may prefer to write their own scripts and/or purchase software solutions but this workflow is intended for a smaller lab or class, one without a bioinformatician or expensive computing power.
All of the scripts and programs for this workflow are open-source and available online for free to ensure that individual researchers and small groups are able to access and utilize the tools necessary to complete the workflow. In general, many available bioinformatic tools are free and open source, but the installation, operation and maintenance of these programs is often complex, requiring specific technical expertise or extensive detailed instructions and best practices in the field remain undefined.
This workflow has been systematically designed and tested to minimize the cost, technical expertise and problems encountered by the user.
