Authors:
Sara Smith (Assistant Professor, Mount Royal University; ssmith6@mtroyal.ca)
LaDeana Hillier (Department of Genome Sciences, Washington University; lhillier@uw.edu)
Chris Balakrishnan (Associate Professor, East Carolina University; balakrishnanc@ecu.edu)
Wes Warren (Professor, University of Missouri; warrenwc@missouri.edu)
Mike Sorenson (Professor, Boston University; msoren@bu.edu)
Tim Sackton (Director of Bioinformatics, Informatics Group, Harvard University; tsackton@g.harvard.edu)
Genome assembly and comparative genomics project with the freckled duck (Stictonetta naevosa; stiNae), ruddy duck (Oxyura jamaicensis; oxyJam), African pygmy-goose (Nettapus auritus; netAur), and black-headed duck (Heteronetta atricapilla; hetAtr) from 10x data using Supernova assembly.
Code is currently being organized and optimized. Code and select data* related to the following analyses can be found in these directories:
01_assemblies: Genome assemblies using Supernova of 10X data and quality checks with BUSCO
02_wga: Generation of a whole genome alignment of Galloanserae genomes using CACTUS
03_ComparativeAugustus: Generation of genome annotations (both de novo and hinted) with Comparative Augustus and quality checks with BUSCO
03_cnee_analyses: Compilation of conserved non-coding elements from Aves and vertebrates and multiple PhyloAcc (https://phyloacc.github.io/) analyses
04_OrthoFinder: Generation of orthogroups using OrthoFinder (https://github.com/davidemms/OrthoFinder)
04_polytomy_resolution: Resolution of phylogenetic polytomy between the focal species using coding and non-coding sequences
05_CompPopGen: VCF generation and quality checks using snpArcher (https://github.com/harvardinformatics/snpArcher), McDonald-Kreitman tests & SnIPRE (Eilertson et al. 2012) for selection using the framework outlined in https://github.com/sjswuitchik/compPopGen_ms/tree/master/MKpipeline, tests for selection using HyPhy (https://github.com/veg/hyphy), demographic inference using Stairway (Liu & Fu 2020), and identification of selective sweeps using SweepFinder2 (DeGiorgio et al. 2016)
When relevant, each directory in this repository will consist of:
- the main scripts numbered in increasing order of operations (e.g., 01_run_setup.sh, 02_run_analyses.sh, 03_parse_output.sh)
- a subscripts directory that contains all the scripts required by the main scripts (e.g., analysis1.py and analysis2.sh used in 02_run_analyses.sh)
- an outputs directory that contains the outputs from the analyses, where file sizes are not restrictive
* select data available through GitHub where files are compatible with GitHub file size permissions. Genome assemblies are available on NCBI (BioProject PRJNA588796).
The archived_analyses directory contains the initial analyses of chromosome-only assemblies; not current.