---
directories:
    work_dir: /usr/local/www/data/private/Glycine/max/Wm82_NJAU.gnm1.ann1
    from_annot_dir: derived
    from_genome_dir: derived
prefixes:
    from_annot_prefix: GWHCAYC00000000.
    from_genome_prefix: GWHCAYC00000000.
collection_info:
    genus: Glycine
    species: max
    scientific_name_abbrev: glyma
    coll_genotype: Wm82_NJAU
    gnm_ver: gnm1
    ann_ver: ann1
    genome_key: N4GV
    annot_key: KM71
readme_info:
    provenance: "The files in this directory originated from https://ngdc.cncb.ac.cn/gwh/Assembly/37536/show. The Genome Warehouse repository is considered the primary repository and authoritative; files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the LegumeInfo and SoyBase projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the LegumeInfo and SoyBase projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please respect any usage restrictions in the present and original repositories, and cite the data appropriately."
    source: "https://ngdc.cncb.ac.cn/gwh/Assembly/37536/show"
    synopsis_genome: Glycine max accession Williams 82 from Nanjing Agricultural University (Wm82-NJAU), genome assebly v1
    synopsis_annot: Annotation 1 for Glycine max accession Williams 82 from Nanjing Agricultural University (Wm82-NJAU), genome assembly v1
    genotype: Wm82_NJAU
    taxid: 3847
    description_genome: "Sequenced using PacBio HiFi, Nanopore ONT ulta-long, and short read Illumina sequencing; assembled with hifisam v0.16.1; minimap2 v2.24; Racon v1.5.0; RagTag v2.1.0"
    chromosome_prefix: Gm
    description_annot: "Gene annotation resources. See full description in supplemental methods at Wang, Lomngfei et al., 2023"
    bioproject: PRJCA015288
    sraproject: 
    dataset_doi_genome: 
    dataset_doi_annot: 
    genbank_accession: 
    original_file_creation_date: 2023-08-19
    local_file_creation_date: 2023-01-17
    dataset_release_date: 2023-02-01
    contributors: Longfei Wang, Mengzhu Zhang, Mengna Li, Xinyu Jiang, Wu Jiao, Qingxin Song
    publication_doi: 10.1016/j.molp.2023.08.012
    citation: "Wang L, Zhang M, Li M, Jiang X, Jiao W, Song Q. A telomere-to-telomere gap-free assembly of soybean genome. Mol Plant. 2023 Nov 6;16(11):1711-1714. doi: 10.1016/j.molp.2023.08.012. Epub 2023 Aug 26. PMID: 37634078."
    publication_title: "A telomere-to-telomere gap-free assembly of soybean genome"
    data_curators: Jacqueline Campbell, Steven Cannon
    public_access_level: public
    license: open
    keywords: "soybean, Wm82, Williams 82, Wm82_NJAU, Wm82-NJAU"
from_to_genome:
  - 
    from: modID.genome.fasta.gz
    to: genome_main.fna
    description: "Primary genome assembly"
original_readme_and_usage:
from_to_genome_as_is:
from_to_cds_mrna:
  - 
    from: modID.CDS.fna.gz
    to: cds.fna
    description: "cds sequences"
  - 
    from: modID.CDS_primary.fna.gz
    to: cds_primary.fna
    description: "cds sequences - primary only"
  - 
    from: modID.transcripts.fna.gz
    to: mrna.fna
    description: "Transcript sequences"
  - 
    from: modID.transcripts_primary.fna.gz
    to: mrna_primary.fna
    description: "Transcript sequences - primary only"
from_to_protein:
  - 
    from: modID.protein.faa.gz
    to: protein.faa
    description: "Protein sequences"
  - 
    from: modID.protein_primary.faa.gz
    to: protein_primary.faa.gz
    description: "Protein sequences - primary only"
from_to_gff:
  -
    from: modID.genes.gff3.gz
    to: gene_models_main.gff3
    description: "Gene models - main"
  -
    from: modID.genes_exons.gff3.gz
    to: gene_models_exons.gff3
    description: "Gene models, with exons"