matthewwiese / apple-phg

A Practical Haplotype Graph (PHG) for apple (Malus domestica)

Apple (Malus domestica) PHG

A Practical Haplotype Graph for apple. 🍎

🚧 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