A Practical Haplotype Graph for apple - read more about this project on the website. 🍎
🚧 A work in progress! 🚧
In the directory where you cloned this repository:
- 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
openjdkpackage.
- 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
- Download the data from NCBI:
./download.sh - Build the PHG:
./build.sh
- Name: ASM211411v1
- FASTA:
data/reference/GCF_002114115.1_ASM211411v1_genomic.fna - GFF:
data/reference/genomic.gff
| 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 |