This contains all of the data used in the study AJMC 2020. including qiime commands, etc.
|-- diadema_ajmc2020
|-- 16S
|-- RawSequences
|-- AllSamples
|-- CategSize
|-- qiimecommands.sh
|-- CytoB
|-- Geneious
|-- de novo
|-- Alignments
|-- Geneious
|-- Velvet
|-- ConsensusSequences
|-- Geneious de novo
|-- Edited
|-- Raw
|-- Tree
|-- Velvet de novo
|-- Edited
|-- Raw
|-- Tree
|-- Trees
|-- Map To References
|-- Alignments
|-- alignref_Contigs
|-- ConsensusSeq
|-- Normalized_ErrorCorrected_RemovedDuplicates
|-- Trees
|-- RawSequences
|-- ReferenceSequences
|-- Trees
|-- README.md
|-- References Thesis.xlx
Learn how to use Geneious: https://www.geneious.com/ | https://www.geneious.com/tutorials/ |
Tutorials used in this study: https://www.geneious.com/tutorials/de-novo-assembly/ | https://www.geneious.com/tutorials/map-to-reference/ |
Learn how to use Mega X: https://megasoftware.net/ |
References:
https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.3732/apps.1400062 |
-
Download & Import sequences from diadema_ajmc2020\CytoB\RawSequences into Geneious.
-
Merge Pair Ends, Trim, Normalize, Error Correct Sequences, Remove Duplicates. [Remove Chimeric Reads???]
|-- diadema_ajmc2020
|-- CytoB
|-- Geneious
|-- Normalized_ErrorCorrected_RemovedDuplicates
- Velvet de novo Assembly of each of the samples
|-- diadema_ajmc2020
|-- CytoB
|-- Geneious
|-- de novo
|-- Velvet de novo
|-- Raw
- Edits: The contigs generated by the de novo were edited to only contain sequences which corresponded close to the length of the gene
|-- diadema_ajmc2020
|-- CytoB
|-- Geneious
|-- de novo
|-- Velvet de novo
|-- Edited
- Alignments: The edited Contigs were aligned within each sample using Geneious Alignment: Global 51
|-- diadema_ajmc2020
|-- CytoB
|-- Geneious
|-- de novo
|-- Alignments
|-- Velvet
- Consensus Sequences: A Consensus Sequence was generated using 0 Majority
|-- diadema_ajmc2020
|-- CytoB
|-- Geneious
|-- de novo
|-- ConsensusSequences
- Consensus Trees A tree was generated with all the samples.
|-- diadema_ajmc2020
|-- CytoB
|-- Geneious
|-- de novo
|-- Velvet de novo
|-- Tree
Tutorial used:
https://docs.qiime2.org/2020.6/ |
https://docs.qiime2.org/2020.6/tutorials/moving-pictures/ |
https://s3-us-west-2.amazonaws.com/qiime2-data/distro/core/virtualbox-images.txt |
To view Qiime files (artifacts (.qza files) and visualizations (.qzv files)) without downloading qiime use: https://view.qiime2.org/
References:
-
Bolyen, Evan, et al. “Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2.” Nature Biotechnology, vol. 37, no. 8, 2019, pp. 852–857., doi:10.1038/s41587-019-0209-9.
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Estaki, Mehrbod, et al. “QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.” Current Protocols in Bioinformatics, vol. 70, no. 1, 2020, doi:10.1002/cpbi.100.
-
Hall, Michael, and Robert G. Beiko. “16S RRNA Gene Analysis with QIIME2.” Methods in Molecular Biology Microbiome Analysis, 2018, pp. 113–129., doi:10.1007/978-1-4939-8728-3_8.
Workflow:
QIIME2 Commands used can be found in diadema_ajmc2020\16S\qiimecommands.sh
-
Import Data
-
Visualize Data Files Generated
allsamplesimport.qzv
- Filter
allsamplesimportdemux-filtered.qza
allsamplesimportdemux-filter-stats.qza
- Deblur & Generate Feature Table
allsamplesimportrep-seqs-deblur.qza
allsamplesimporttable-deblur.qza
allsamplesimportdeblur-stats.qza
- Summary Stats
allsamplesimportdemux-filter-stats.qzv
allsamplesimportdeblur-stats.qzv
- Summary Feature Table $ Feature Sequence Data
seaurchinfeaturetableallsamples.qzv
sequences.qzv
- Generate a Phylogenetic Tree
aligned-rep-seqs.qza
masked-aligned-rep-seqs.qza
unrooted-tree.qza
rooted-tree.qza
- Alpha & Beta Diversity
core-metrics-results (FOLDER)
- Exploring Microbial Composition with Metadata
core-metrics-results/faith-pd-group-significance.qzv
core-metrics-results/evenness-group-significance.qzv
- Permanova
core-metrics-results/unweighted-unifrac-reefhabitat-significance.qzv
core-metrics-results/unweighted-unifrac-location-significance.qzv
- Emperor Plots by Metadata
core-metrics-results/unweighted-unifrac-emperor-size.qzv
core-metrics-results/bray-curtis-emperor-size.qzv
- Alpha Rarefaction Plotting
alpha-rarefaction.qzv
- Taxonomic Analysis
taxonomy.qza
taxonomy.qzv
taxa-bar-plots.qzv
- Group by Metadata
locationseaurchintable.qza
- Merge by Metadata.
grouped-taxa-bar-plots.qzv