ngs-assembly-phylogenetics-labs
A series of laboratory modules designed to walk undergraduate students through the assembly of a chloroplast genome using NGS sequence data, followed by phylogenetic analysis of nucleotide data.
https://github.com/dkoenemann/ngs-assembly-phylogenetics-labs
Science Score: 26.0%
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A series of laboratory modules designed to walk undergraduate students through the assembly of a chloroplast genome using NGS sequence data, followed by phylogenetic analysis of nucleotide data.
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Metadata Files
README.md
NGS-Assembly-Phylogenetics-Labs
1_IntroBioinformaticsTools.docx - How to activate or access the Linux terminal for Mac, Windows, and Chromebook. The Chromebook portion in particular is exploratory. I have yet to find a way to make these labs work on a Chromebook. Also, difficulties have been encountered in obtaining root privileges on Macs.
1Files.zip - The files manipulated in 1IntroBioinformaticsTools.docx
2_NGSIntroCleaning.docx - A basic introduction to navigating and entering commands in the terminal. Finding the Desktop when using the Ubunut WSL can be difficult. This lab module will also show students how to download sequence data from GenBank and from the Sequence Read Archive (SRA). Students will also clean the SRA reach archive data and conduct quality checks.
3_NGSPlastomeAssembly - The actual assembly of the chloroplast genome using the SRA reach archive and one plastome as a reference.
3_Coverage.rmd - An R notebook containing some code for generating statistics to assess the assembly
4_PlastomeAnotation.docx - A module showing stduents how to use web tools to annotate the assembled chloroplast genome.
5_PhylogeneticsBioinformatics.docx - A module showing students how to use BEAST to analyze assembled genomes phylogenetically. The data used in this module is only a section of a plastome to help the task fit inside of a lab period.
AllSeqs.fasta - Data used in the module 5_PhylogeneticsBioinformatics.docx