Draft genome of the staghorn coral Acropora millepora
The draft assembly was constructed from a combination of PacBio and Illumina paired-end reads with 10X Genomics barcodes. Feel free to use the assembly and publish results that rely on it, but be aware that it is a work in progress. We hope to release updated versions, so please email us if you identify errors in your own analyses. For all questions, please send us an email at corals.columbia AT gmail.com and include your name and institution. See Methods for a description of the assembly and annotation pipelines.
To download the genome assembly: Download
Scripts and data used in analyses: Github
Stats (Version 2.01 Dec 6 2019) – Scaffold N50: 19.84 Mb (Contig N50: 1.08 Mb); Average length: 556.6 kb; Total length: 475.4 mb; # of scaffolds: 854; # of gene models: 28,188
The data for Baker et al. ‘Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates’ (2017) are available as:
The data for Moorjani, Amorim et al. ‘Variation in the molecular clock in primates’ (2016) are available as:
The data for Singhal, Leffler et al. ‘Stable recombination hotspots in birds’ (2015) are available as:
Unpublished sequences of the PRDM9 ZF in primates: PRDM9_summary, readme, fasta sequences.
TroX: a R package for Kermany et al. (2014)
Shared SNP coordinates for Leffler et al. (2013) Science.
Table S1 for Meyer et al. (2012) Genetics.
For the data reported in Auton et al. (2012) Science:
The sequence data (in BAM file format), variant calls (in VCF file format), genetic maps, and sequenced PRDM9 alleles are available for download over anonymous FTP from ftp://birch.well.ox.ac.uk/. The BAM files are available from the Short Read Archive,
| SUBMISSION_ID | STUDY_ACCESSION | STUDY_ALIAS | RELEASE_DATE |
| ERA191030 | ERP002171 | PanMap | 25-Mar-2013 |
Given the large number of repeat classes, we do not show recombination rates around all possible repeats in our paper. However, recombination rates around any repeat with more than 200 occurrences (after thinning nearby copies) of interest can be viewed using an interactive online viewer. The viewer can be accessed here.
Supplementary Material S2 for Fledel-Alon et al. (2011) PloS One.
Kevin Bullaughey’s regulatory evolution simulation software (Changes in selective effects over time facilitate turnover of enhancer sequences) described in Bullaughey, K. (2011) Genetics, is available here.
Ryan Hernandez’s SFS_CODE (Selection on Finite Sites under Complex Demographic Effects), described in Hernandez (2008) Bioinformatics is available here.
Supplementary materials for Coop et al. (2008) Science.
Carole Ober’s website on mapping in the Hutterites:http://www.genes.uchicago.edu/hutterite/home.html
Tar file including MIMAR program, goodness of fit test and readme files for Becquet and Przeworski (2007) Genome Research. Complete documentation is available here for an introduction.
Supplementary materials for Teshima et al. (2006) Genome Research: PDF file.
For the program described in Przeworski et al. (2005) Evolution, SELSIMSTAND, contact Graham Coop.
Supplementary materials for Ptak et al. (2004) Genetics: PDF file.
Program described in Przeworski (2003) Genetics, available upon request to Molly Przeworski (mp3284 at columbia.edu).
Supplementary materials for Ptak and Przeworski (2002) TIG: Tab-delimited text file.