NRM DNA lab - Standard Workflows

• Last modified: tis apr 30, 2024 11:01
• Sign: JN

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Personal Checklist

To be able to work smoothly with the workflows, there are a number of accounts and settings that needs to be in place for each person. Please go through the personal checklist (doc/checklist/README.md) and send feedback on the progress to the other lab members.

Create a Project Repository on GitHub

To ensure reproducibility, it is important to document all steps of the data management and analysis. A recommended procedure is to create a repository where all text is under version control.

NRM have an organization on GitHub: github.com/Naturhistoriska, and that is an appropriate location to keep repositories.

General procedure (please see doc/github/README.md for details):

1. Create a private repository on github for the project. Name it short but kind-of human readable, e.g., johan-n-snakes.
2. Add the GitHub Team NRM-DNA-lab as collaborators on the repository. If practical, add also the PI (this requires that the PI has a github account, and that he or she is added to the Naturhistoriska github organization).

Securing Meta Data from User

Meta data about the samples. This information is crucial in the workflows, and will be used in the database submission step. Important is to start a project by providing the user with a sample sheet to be filled in before starting any lab work. The same sheet can then be used for ordering data from NGI, running bioinformatic workflows, and submitting relevant data to public databases.

Please see the instructions for meta data here: doc/metadata/README.md.

Ordering Sequences from SciLifeLab/NGI

Note: current supplier of NGS data are the NGI-platforms in Stockholm and Uppsala. Both are under SciLifeLab (https://www.scilifelab.se/units/ngi) but they differ in how sequences are ordered and delivered, as well in what machines are available.

See descriptions in doc/ngi/README.md.

Data Download from NGI using DDS

See descriptions in doc/dds/README.md.

Copy Files Between Computers

See description in doc/ssh/README.md.

Quality Control of Sequence Data

A standard quality assessment of sequences are often made by the sequence provider. Sometimes, however, it may be relevant to do this on your own.

See descriptions in doc/qc/README.md.

Data Cleaning, Merging, etc

Note: this step may or may not be necessary depending on the choice of downstream analyses.

See description in doc/cleaning/README.md.

Analyses

See doc/analyses/README.md for description.

Data Submission to Public Databases

Sequence data can be submitted to public databases such as Genbank or ENA. This is something that the NRM DNA-lab can assist in doing. A prerequisite for doing this is that the user submitted a properly filled out sample sheet in the very start of the project (see Metadata section.

Example for submitting short-read (Illumina) data to ENA: doc/ena/README.md.