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Apple (Malus domestica) PHG

A Practical Haplotype Graph for apple - read more about this project on the website. 🍎

🚧 A work in progress! 🚧

Running

In the directory where you cloned this repository:

  1. Create and activate the Conda environment: conda env create -f environment.yml && conda activate phgv2-conda
    • PHG v2 does not yet have a Conda package, so follow these instructions to install it; Java 17+ is required, which is installed via the openjdk package.
  2. Download the data from NCBI: ./download.sh
  3. Build the PHG: ./build.sh

Data

Reference

  • Name: ASM211411v1
  • FASTA: data/reference/GCF_002114115.1_ASM211411v1_genomic.fna
  • GFF: data/reference/genomic.gff

Founder Assemblies

Name Date Species Source Database Assembly Level Assembly Method Genome Size Genome Coverage Sequencing Technology File
ASM411538v1 Jan 29, 2019 M. domestica GenBank Chromosome FALCON v. 0.4 660.5 Mb 100.0x PacBio RSII data/assemblies/GCA_004115385.1_ASM411538v1_genomic.fna
PFR_Mdom_1.0 Mar 17, 2022 M. domestica GenBank Chromosome MaSuRCA v. 1.0 754.7 Mb 200.0x Illumina HiSeq; PacBio RSII data/assemblies/GCA_022606005.1_PFR_Mdom_1.0_genomic.fna
Malus_domestica_Gala.pri Feb 6, 2023 M. domestica GenBank Chromosome DeNovaMAGIC v. 3 652.4 Mb 707.0x Illumina data/assemblies/GCA_028456005.1_Malus_domestica_Gala.pri_genomic.fna
Malus_domestica_Gala.altA Feb 6, 2023 M. domestica GenBank Chromosome DeNovaMAGIC v. 3 657.7 Mb 707.0x Illumina data/assemblies/GCA_028456015.1_Malus_domestica_Gala.altA_genomic.fna
Malus_domestica_Gala.altB Feb 6, 2023 M. domestica GenBank Chromosome DeNovaMAGIC v. 3 577.2 Mb 707.0x Illumina data/assemblies/GCA_028456065.1_Malus_domestica_Gala.altB_genomic.fna
drMalDome10.2 Oct 21, 2022 M. domestica GenBank Chromosome various 648.2 Mb 31.0x PacBio,Illumina,Arima data/assemblies/GCA_916050505.2_drMalDome10.2_genomic.fna
drMalDome11.2 Oct 21, 2022 M. domestica GenBank Chromosome various 652.8 Mb 42.0x PacBio,Illumina,Arima data/assemblies/GCA_916612005.2_drMalDome11.2_genomic.fna
drMalDome58.3 Oct 25, 2022 M. domestica GenBank Chromosome various 642.6 Mb 24.0x PacBio,Illumina,Arima2 data/assemblies/GCA_916615275.3_drMalDome58.3_genomic.fna
drMalDome5.3 Oct 21, 2022 M. domestica GenBank Chromosome various 646.8 Mb 25.0x PacBio,Illumina,Arima data/assemblies/GCA_916615385.2_drMalDome5.3_genomic.fna
ASM2079583v1 Nov 8, 2021 M. sieversii GenBank Chromosome String graph v. 1 682.9 Mb 149.1x Nanopore data/assemblies/GCA_020795835.1_ASM2079583v1_genomic.fna
Malus_sieversii.pri Feb 6, 2023 M. sieversii GenBank Chromosome DeNovaMAGIC v. 3 667.7 Mb 780.0x Illumina data/assemblies/GCA_028456125.1_Malus_sieversii.pri_genomic.fna
Malus_sieversii.altA Feb 6, 2023 M. sieversii GenBank Chromosome DeNovaMAGIC v. 3 653.6 Mb 780.0x Illumina data/assemblies/GCA_028456135.1_Malus_sieversii.altA_genomic.fna
Malus_sieversii.altB Feb 6, 2023 M. sieversii GenBank Chromosome DeNovaMAGIC v. 3 612.2 Mb 780.0x Illumina data/assemblies/GCA_028456155.1_Malus_sieversii.altB_genomic.fna
drMalSylv7.2 Jul 6, 2022 M. sylvestris GenBank Chromosome See comment on NCBI 641 Mb 25.0x See comment on NCBI data/assemblies/GCF_916048215.2_drMalSylv7.2_genomic.fna
drMalSylv7.3 Oct 25, 2022 M. sylvestris GenBank Chromosome various 641 Mb 25.0x PacBio,Illumina,Arima data/assemblies/GCA_916048215.3_drMalSylv7.3_genomic.fna
Malus_sylvestris.pri Feb 6, 2023 M. sylvestris GenBank Chromosome DeNovaMAGIC v. 3 661 Mb 623.0x Illumina data/assemblies/GCA_028456055.1_Malus_sylvestris.pri_genomic.fna
Malus_sylvestris.altA Feb 6, 2023 M. sylvestris GenBank Chromosome DeNovaMAGIC v. 3 627.6 Mb 623.0x Illumina data/assemblies/GCA_028456085.1_Malus_sylvestris.altA_genomic.fna
Malus_sylvestris.altB Feb 6, 2023 M. sylvestris GenBank Chromosome DeNovaMAGIC v. 3 601.4 Mb 623.0x Illumina data/assemblies/GCA_028456105.1_Malus_sylvestris.altB_genomic.fna