odgi-paper

resources

The input graphs can be found at https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=pangenomes/scratch/2021_11_16_pggb_wgg.88/.
The GRCh38 FASTAs we used can be found at https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/.
The corresponding GTF file at https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ncbiRefSeq.gtf.gz.

building the manuscript

# Dependencies
sudo apt-get -y install texlive texlive-latex-recommended \
        texlive-pictures texlive-latex-extra texlive-fonts-extra \
        texlive-science

sudo apt install graphviz

git clone https://github.com/pangenome/odgi-paper
cd odgi-paper/manuscript && make -k

Bx author instructions

https://academic.oup.com/bioinformatics/pages/instructions_for_authors

Original papers: approximately 5,000 words The abstracts should be succinct and contain only material relevant to the headings. A maximum of 150 words is recommended.