California condor genome data and resources

Genome assembly for the California condor, genotype data for two California condors and two related species (Andean condor and turkey vulture), and supporting files. See "Genome-wide diversity in the California condor tracks its prehistoric abundance and decline," by Robinson et al. (2021) for full details. Also see https://10.5281/zenodo.4680034 for processing and analysis code. Samples:<br> <strong>CRW1112</strong> California condor (Studbook #593)<br> <strong>CYW1141</strong> California condor (Studbook #309)<br> <strong>VulGry1</strong> Andean condor (ISIS 417)<br> <strong>BGI_N323</strong> Turkey vulture (SAMN02319050, from https://doi.org/10.1126/science.1251385) Files:<br> <strong>gc_PacBio_HiC.fasta</strong> California condor genome sequence. <strong>gc_PacBio_HiC_scaffold_chr_key.txt</strong> Key giving the chromosomal identity of scaffolds in the California condor genome assembly (where known). <strong>gc_PacBio_HiC_repeats*.bed</strong> Coordinates of repeats in the California condor genome identified with Tandem Repeats Finder (TRF, https://tandem.bu.edu/trf/trf.html) and WindowMasker (WM, https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker). <strong>*.vcf.gz, *.vcf.gz.tbi</strong> Raw VCF files plus indexes for each sample aligned to reference gc_PacBio_HiC.fasta. <strong>*cpgIslands*.bed</strong> Coordinates of CpG islands in gc_PacBio_HiC.fasta. Coordinates including and excluding CpG islands in repeats are provided. <strong>*.over.chain.gz, *.rbest.chain.gz</strong> Chain files for liftOver (https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64). Named as FROM.TO.TYPE.chain.gz. The "rbest" chains represent the reciprocal best alignments between both genomes. ASM69994v1 is the turkey vulture genome assembly, galGal6 is the chicken genome assembly. <strong>ismc_CYW1141.rho.*.bed</strong> Bed files containing coordinate ranges and rho/bp inferred with iSMC (https://github.com/gvbarroso/iSMC) using California condor #309. Intervals of 1 kb and 1 Mb are provided. <strong>*.psmc, *.msmc, *.msmc2</strong> Output files from PSMC (https://github.com/lh3/psmc), MSMC (https://github.com/stschiff/msmc), and MSMC2 (https://github.com/stschiff/msmc2). <strong>ROH*.bed</strong> Coordinates of runs of homozygosity (ROH) &gt;=1 Mb in each California condor sample, identified with Plink (v1.9, https://www.cog-genomics.org/plink/).