This page demonstrates all the analyses in the paper, titled "A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes".

Genome assembly

1) Using falcon to do the pacbio assembly
    bash ./01.Pacbio_assembly/falcon.sh
2) 10x scaffolding
# Reads pre_process.
  bash ./02.10x_scaffolding/01.Reads/01_pre_process.sh
# Using Scaff10x for the initial scaffolding.
  bash ./02.10x_scaffolding/02.Scaff10x/02_Scaff10x.sh
# Using ARCS and LINKS for the second round of scaffolding.
  bash ./02.10x_scaffolding/03.ARCS_LINKS/03_Longranger_ARCS_LINKS.sh
3) HiC scaffolding
# DovetailGenomics scaffolding. Available HiRise software is at https://github.com/DovetailGenomics/HiRise_July2015_GR.
# Using juicer to produce hic matrix.
  bash ./03.HiC/02.Juicer.sh
# Using 3D-DNA for further scaffolding.
  bash ./03.HiC/03.3D_DNA.sh
# Using juicerbox for manually correction.

Genome annotation

1) RepeatMask
    bash ./01.RepeatMask/01.RepeatModeler.sh & bash ./01.RepeatMask/02.RepeatMasker.sh
    # tandem repeat detection using trf.
    bash ./01.RepeatMask/03.TandomRepeat.sh
2) The first round of maker
    bash ./02.Maker_R1/round1.sh
3) Gene model preduction
    bash ./03.Augustus_SNAP/Augustus.sh & bash ./03.Augustus_SNAP/SNAP.sh
4) The second round of maker
    bash ./04.Maker_R2/round2.sh
5) Using PASA to correct the gene annotation
    bash ./05.PASA/Emu.Trinity.sh & bash ./05.PASA/02.Emu.PASA.sh
# Details can be found in https://github.com/umd-byob/presentations/tree/master/2015/0324-RepeatMasker-RepeatModeler and https://gist.github.com/darencard/bb1001ac1532dd4225b030cf0cd61ce2.

Comparative genomics

1) Pairwise alignment
# Using lastal to do pairwise genome alignments.
  bash ./01.Pairwise_alignment/Emu.Chicken.PairwiseAlign.sh
2) Synteny visualization
  circos ./02.Synteny_visualization/Turtle.Emu.circos.conf
3) Rearrangement detection
# Merge the local small syntenic blocks produced by lastal.
  bash ./03.Rearrangement_detection/01.Block_Merge.sh
# Classify genomic rearrangements (INV, TRANS and INV_TRANS)
  bash ./03.Rearrangement_detection/02.Rearrangement_Detection.sh

Hi-C analysis

1) Generating HiC matrix with HiCExplorer & HiCPro
  bash ./01.HiC_matrix/01.HiCExplorer_P1.sh & bash ./01.HiC_matrix/01.HiCExplorer_P2.sh
  bash ./01.HiC_matrix/02.HiC-Pro.sh
2) TAD-calling and plot using HiCExplorer
  bash ./02.HiC_tad/1.TAD_detection.sh & bash ./02.HiC_tad/02.TAD_plot.sh
3) AB compartment
# AB compartments were generated using cooler.
  bash ./03.AB_compartment/01.PCA.sh
# Compartmentalization using cooler.
  bash ./03.AB_compartment/02.Compartmentalization.sh
# Calculating compartment strength
  bash ./03.AB_compartment/03.Compartment_strength.sh

Sex chromosome evolution

1) ZW similarity
  Details can be found at https://github.com/lurebgi/BOPsexChr.
2) Using genewise to evaluate the degeneration of W-linked genes
  bash ./02.W_degeneration/Genewise.sh
3) ZW HiC interaction
  bash ./03.ZW_HiC_interaction/ZW.Interaction.Window.sh