Example Information for sppIDer

The genus Saccharomyces can be used as a simple test case. Below describes the files needed and where to find them.
The end of the sppIDer manual had how to run the sppIDer pipeline with these examples.

Example for making a combination reference genome

This step requires all the reference genomes of interested and a tab seperated file that keys the names of the fastas to a unique identifier. Here is an example that can be used for Saccharomyces.
Below is a list of Saccharomcyes reference genomes and where to find them.

Reference Genomes:

The published S. uvarum genome (Scannell and Zill et al 2011) had chromosome X swapped with chromosome XII.

References:

Baker E, Wang B, Bellora N, Peris D, Hulfachor AB, Koshalek JA, Adams M, Libkind D, Hittinger CT. 2015. The genome sequence of Saccharomyces eubayanus and the domestication of lager-brewing yeasts. Mol. Biol. Evol. 32:2818–2831.
Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, et al. 2009. Population genomics of domestic and wild yeasts. Nature 458:337–341.
Liti G, Nguyen Ba AN, Blythe M, Müller CA, Bergström A, Cubillos FA, Dafhnis-Calas F, Khoshraftar S, Malla S, Mehta N, et al. 2013. High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. BMC Genomics 14:1-14.
Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT. 2011. The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 1:11–25.

Example test data

References:

Almeida P, Gonçalves C, Teixeira S, Libkind D, Bontrager M, Masneuf-Pomarède I, Albertin W, Durrens P, Sherman DJ, Marullo P, et al. 2014. A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat. Commun. 5:4044.
Peris D, Langdon QK, Moriarty R V, Sylvester K, Bontrager M, Charron G, Leducq J, Landry CR, Libkind D, Hittinger CT. 2016. Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus. PLoS Genet. 12: e1006155.

Example outputs

Files in exampleOutputs. Each set of input fastqs have corresponding output files.
File Suffix | Description
- SRR*_sppIDerRun.info | A text file that contains the options and inputs for that run and the time to run.
- SRR*_MQsummary.txt | Text file with summary of how many and how well reads map to each genome.
- SRR*_plotMQ.pdf | Plot of reads mapped per genome and Mapping Quality per genome.
- SRR*_speciesAvgDepth-d.txt | Text file summary of coverage for each species including: mean, relativeMean (speciesMean/globalMean), max, and median coverage.
- SRR*_speciesDepth.pdf | Plot of coverage by species.
- SRR*_sppIDerDepthPlot-d.pdf | Plot of coverage by genome split into 10,000 windows.

Example mitochondrial inputs

Saccharomyces can also be used to test mitoSppIDer. Two text files are provided as examples of the required user provided keys to make a combined reference genome and gff. Below are links to a mitochondrial genome for each Saccharomyces species.
mitoRefKey.txt - Tab separated text file to match mitochondrial (mito) reference genome with desired unique name.
mitoGFFKey.txt - Tab separated text file to match mitochondrial (mito) reference GFF with desired unique name.

Species Files:

Some mitochondrial genes are missing from the published gffs and will have to be annotated by hand if they are desired.

References:

Baker E, Wang B, Bellora N, Peris D, Hulfachor AB, Koshalek JA, Adams M, Libkind D, Hittinger CT. 2015. The genome sequence of Saccharomyces eubayanus and the domestication of lager-brewing yeasts. Mol. Biol. Evol. 32:2818–2831.
Foury F, Roganti T, Lecrenier N, Purnelle B. 1998. The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett. 440:325–331.
Procházka E, Franko F, Poláková S, Sulo P. 2012. A complete sequence of Saccharomyces paradoxus mitochondrial genome that restores the respiration in S. cerevisiae. FEMS Yeast Res. 12:819–830.
Sulo P, Szabóová D, Bielik P, Polákova S, Šoltys K, Jatzová K, Szemes T. 2017. The evolutionary history of Saccharomyces species inferred from completed mitochondrial genomes and revision in the 'yeast mitochondrial genetic code'. DNA Res. 24:571-583.