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04_wga

README.md

Whole genome alignment

We used progressiveCactus to generate a whole genome alignment from 35 bird genomes and 7 non-avian reptile outgroups. Our version of progressiveCactus uses a modified version of jobTree in order to work with SLURM.

Alignment steps

  1. Selection of genomes: in addition to our 10 new palaeognath genomes, we focused on other bird genomes of relatively high quality measured by both contiguity statistics (contig and scaffold N50) and completeness (BUSCO). We make a few exceptions for important outgroups. The full list of species used, including assembly versions, is in species_list.tsv, and the script to fetch them from NCBI is get_genomes.sh (in the progressiveCactus subdirectory).

  2. Guide tree generation: the code in the branchlengths subdirectory includes the methods and data sources for generating the guide tree we used for our whole genome alignment. The R script compute_br_for_cactus.R contains all the information and scripts needed to generate our final branch lengths.

  3. Whole-genome alignment: the code in the progressiveCactus subdirectory includes our configuration files and scripts to run progressiveCactus. For more details about progressiveCactus, please see here.

Note about ostrich

We used the superscaffolds produced by BGI for our whole genome alignment. All other species are either from NCBI or newly assembled for this project.

CNEEs

We identified CNEEs using PHAST (02_ce_id). These were then loosely assigned to genes based on the nearest transcription start site (03_cnee_annotation).

BEDS

Final bed files with CNEE coordinates, both galGal4 and lifted-over to galGal5, are available for both UCSC and NCBI chromosome ids:

  • 03_ce_annotation/cnees.galGal4NCBI.bed
  • 03_ce_annotation/cnees.galGal4UCSC.bed
  • 03_ce_annotation/cnees.galGal5NCBI.bed
  • 03_ce_annotation/cnees.galGal5UCSC.bed

The full set of conserved elements (not filtered for length, and including those that overlap exons) is available only for NCBI galGal4 coordinates:

  • 03_ce_annotation/galGal4_cons_element.bed

Files indicating the nearest TSS for each CNEE (using NCBI gene annotations) are also provided as:

  • 03_ce_annotation/cnees.galgal4.annotation
  • 03_ce_annotation/cnees.galgal5.annotation