Genome_assembly_annotation

Authors: Zhou wu090& Langqing liu194

Major Update: 20220322

The code should be used with your own input to replace the test.files

📊 Assessment

Genome_statistic

N50, N90 Calculation

RepeatMask

# Run RepeatModeler to generate repeat library
RepeatModeler -ninja_dir ${ninja_path} -pa ${threads} -LTRStruct -database ${PREFIX}_masked

# Run RepeatMasker with repeat library to mask repeats in genome and output results in GFF format
export BLASTDB_LMDB_MAP_SIZE=100000000
RepeatMasker -pa ${threads} -lib ${PREFIX}-families.fa -xsmall -s -pa 4 -gff -dir ${OUTPUT}/repeatmasker/ ${GENOME}

😹 Kmer

Kmer_jellyfish.sh Using jellyfish to calculate the Kmer

✂️ Purge_dups

Purge_post

Ater Purge_dups, I used my python code to select those regions at the end of the begining of a scaffold. See Purge_post/

Parse_purge_dups_opt.py, test.bed, test.chr_size, and test.out

python3 Parse_purge_dups.py -i test.bed -s test.chr_size -o test.out

➰ Mitochondrial DNA

run_mito_mapp.sh and remove_fa.sh

📌 Busco

BUSCO.sh

busco -i test.fa -o  test_vertebrata_busco --out_path ./busco -m genome -l vertebrata_odb10 -c 16 -f

📐 Dot-plot Comparative genome

make_dot_nucmur.sh and mummerCoordsDotPlotly.R (adopted from tpoorten/dotPlotly )

🎺 Genome annotation pipeline(see below)

👀 Scripts to create figures in paper

Fig1_circos.R, Fig2_dot.R, Fig3_BUSCO.R, Fig4_chr_features.R

Pipeline

%%{init: {'theme':'forest'}}%%

stateDiagram
    #[*] --> genome
    #genome --> [*]
    Short_read_polishing --> genome
    OmniC --> genome
    PacBio --> genome
    #genome --> repeatmask
    genome --> RNAseq
    RNAseq --> Splice_junctions
    Splice_junctions --> transdecoder
    transdecoder --> protein_prediction
    genome --> Isoseq
    genome --> ab_initio 
    genome --> Braker_ETP
    Protein --> Braker_ETP
    RNAseq --> Braker_ETP
    Isoseq --> EVM
    ab_initio  --> EVM
    Braker_ETP --> EVM
    transdecoder --> EVM
    protein_prediction --> EVM
    

Cite this article

Wu, Z., Miedzinska, K., Krause, J.S. et al. A chromosome-level genome assembly of a free-living white-crowned sparrow (Zonotrichia leucophrys gambelii). Sci Data 11, 86 (2024). https://doi.org/10.1038/s41597-024-02929-6