Merge pull request #1 from FGPLab/rc1

Release candidate 1

README.md

@@ -1,2 +1,28 @@
-# cydrasil
-A comprehensive phylogenetic tree for cyanobacterial 16s sequences used for sequence placement
+# **Cydrasil:** A comprehensive phylogenetic tree of cyanobacterial 16s rRNA gene sequences
+Daniel Roush, Ana Giraldo-Silva, Vanessa M. C. Fernandes, Nathali Maria Machado de Lima, Corey Nelson, Sam McClintock, Sergio Velasco Ayuso, Kevin Klicki, Blake Dirks, Watson Arantes, Kira Sorochkina, and Ferran Garcia-Pichel
+
+<sup>1</sup>School of Life Sciences, Arizona State University, 85282 Tempe, Arizona, USA
+
+<sup>2</sup>Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, 85282 Tempe, Arizona, USA
+
+## **Methods**
+This is a phylogenetic tree containing 980 cyanobacterial sequences, downloaded from NCBI and used for placement of sequence variants (sOTUs) from 16s rRNA gene amplicon studies. 
+The reference alignment was generated using SSUALIGN<sup>1</sup> with default parameters and then masked using SSUMASK with the automatically computed alignment confidence values (posterior probabilities). A maximum-likelihood phylogenetic tree was then generated using the RAxML-HPC2<sup>2</sup> Workflow on XSEDE (8.2.9) on the CIPRES Science Gateway<sup>3</sup>. The ML + thorough bootstrap workflow was used with the following modified parameters: 1000 bootstraps (-N 1000) and the GTRGAMMA model. All other parameters were left at default values.  
+
+## **Use**
+A FASTA file containing sequences of interest (typically the reference sequence file from Qiime1/2) is aligned to the reference alignment using an alignment tool. We use PaPaRa<sup>4</sup> alignment and the repository contains a phylip (.phy) alignment to use with PaPaRa. 
+```
+papara -t cydrasil-rc1-bipartitions-tree-1000.nwk -s cydrasil-rc1-alignment-phylip.phy -q ref-seqs.fasta -n combined-aln
+```
+The output combined alignment is then used as the input into the Evolutionary Placement Algorithm function of RAxML 8. 
+```
+raxml-HPC ¬-f v ¬-s papara_alignment.combined-aln -¬t cydrasil-rc1-bipartitions-tree-1000.nwk -¬m GTRGAMMA -¬n SeqPlacements 
+```
+To visualize the new phylogenetic tree containing the sequences of interest, the placement file (_RAxML_portableTree.SeqPlacements.jplace_) is uploaded onto [iTOL] (https://itol.embl.de/)<sup>5</sup>. Placements are a dataset within iTOL and can be toggled. Nodes with sequences of interest are visualized with red spheres and clicking a node will show a breakdown of sequence ids and the corresponding confidence values for that node. 
+
+## **References**
+1. 	Nawrocki E. 2009. Structural RNA Homology Search and Alignment Using Covariance Models. Washington University School of Medicine.
+2. 	Stamatakis A. 2014. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313.
+3. 	Miller MA, Pfeiffer W, Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. 2010 Gatew Comput Environ Work GCE 2010.
+4. 	Berger SA, Stamatakis A. 2011. Aligning short reads to reference alignments and trees. Bioinformatics 27:2068–2075.
+5. 	Letunic I, Bork P. 2016. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 44:W242–W245.