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config
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#
# This file is a part of PED; Config file for Polymorphic Edge Detection.
#
# Copyright (C) 2017 National Agriculture and Food Research Organization. All Rights Reserved.
#
# License: refer to https://github.com/akiomiyao/ped
#
#
# Structure of config file
#
# Name data_type values
# Items are separated by tab.
#
# data_type values
# description short note of reference genome.
# wget URL of reference genome data with fasta format
# chromosome start end non-numerical names
#
# If all names of chromosome are not numerical, start and end are set to 0,
# and names should be set at fifth or more columns.
#
hg38 description Human (Homo sapiens) Genome Reference Consortium Human Build 38
hg38 wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
hg38 chromosome 1 22 X Y
hg19 description Human (Homo sapiens) Genome Reference Consortium Human Build 19
hg19 wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz
hg19 chromosome 1 22 X Y
IRGSP1.0 description Rice (Olyza sativa L. cv. Nipponbare) version 1.0
IRGSP1.0 wget https://rapdb.dna.affrc.go.jp/download/archive/irgsp1/IRGSP-1.0_genome.fasta.gz
IRGSP1.0 chromosome 1 12
TAIR10 description Arabidopsis thaliana version TAIR10
TAIR10 wget ftp://ftp.ensemblgenomes.org/pub/plants/release-41/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.gz
TAIR10 chromosome 1 5
GRCm38 description Mouse (Mus musculus) Genome Reference Consortium Mouse Build 38
GRCm38 wget ftp://ftp.ensembl.org/pub/release-91/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz
GRCm38 chromosome 1 19 X Y
Gmax275v2.0 description Soybean (Glycine max) genome project assemble version 2
Gmax275v2.0 wget Login to https://phytozome.jgi.doe.gov/; Download Gmax_275_v2.0.fa.gz; Save the gz file into Gmax275v2.0 directory.
Gmax275v2.0 chromosome 1 20
WBcel235 description Caenorhabditis elegans WBcel235
WBcel235 wget ftp://ftp.ensembl.org/pub/release-98/fasta/caenorhabditis_elegans/dna/Caenorhabditis_elegans.WBcel235.dna.toplevel.fa.gz
WBcel235 chromosome 0 0 I II III IV V X
dmel626 description Drosophila melanogaster release 6.26
dmel626 wget ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6.26_FB2019_01/fasta/dmel-all-chromosome-r6.26.fasta.gz
dmel626 chromosome 0 0 2L 2R 3L 3R 4 X Y
danRer11 description Zebrafish (Danio rerio) Genome Reference Consortium Zebrafish Build 11
danRer11 wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/035/GCF_000002035.6_GRCz11/GCF_000002035.6_GRCz11_genomic.fna.gz
danRer11 chromosome 1 25
IWGSC1.0 description Wheat (Triticum aestivum L. cv. Chinese Spring) Version 1.0
IWGSC1.0 wget https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Assemblies/v1.0/iwgsc_refseqv1.0_all_chromosomes.zip
IWGSC1.0 file 161010_Chinese_Spring_v1.0_pseudomolecules.fasta
IWGSC1.0 chromosome 0 0 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D 7A 7B 7D
Fielder1 description Wheat (Triticum aestivum L. cv. Fielder) Version 1
Fielder1 wget https://shigen.nig.ac.jp/wheat/komugi/genome/download/201216_Fielder_pseudomolecules_V1+unanchored_contigs.fasta.gz
Fielder1 chromosome 0 0 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A 4B 4D 5A 5B 5D 6A 6B 6D 7A 7B 7D
IBSC2 description Barley (Hordeum vulgare L. cv. Molex) Release 47
IBSC2 wget ftp://ftp.ensemblgenomes.org/pub/plants/release-47/fasta/hordeum_vulgare/dna/Hordeum_vulgare.IBSC_v2.dna.toplevel.fa.gz
IBSC2 chromosome 0 0 1H NOP 2H 3H 4H 5H 6H 7H
SL3 description Tomato (Solanum lycopersicum cv. Heinz 1706) Build 3.0
SL3 wget ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/S_lycopersicum_chromosomes.3.00.fa.tar.gz
SL3 chromosome 0 0 NOP 1 2 3 4 5 6 7 8 9 10 11 12
LJ3 description Lotus japonicus MG20 v3.0 (Download from https://lotus.au.dk/data/download into LJ3 directory)
LJ3 file Lotusjaponicus_MG20_v3.0_genome.fa
LJ3 chromosome 0 0 0 1 2 3 4 5 6
B73v4 description Corn (Zea mays B73) RefGen v4
B73v4 wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_000005005.6_B73_RefGen_v4/GCA_000005005.6_B73_RefGen_v4_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/
B73v4 chromosome 1 10
Bomo description Silkworm (Bombyx mori) Genome assembly (Nov.2016)
Bomo wget http://silkbase.ab.a.u-tokyo.ac.jp/pub/Bomo_genome_assembly.fa.gz
Bomo chromosome 1 28
UMD3.1 description Cow (Bos taurus L1 Dominette 01449) UMD 3.1
UMD3.1 wget http://128.206.12.216/drupal/sites/bovinegenome.org/files/data/umd3.1/UMD3.1_chromosomes.fa.gz
UMD3.1 chromosome 0 0 10 11 12 13 14 15 16 17 18 19 1 20 21 22 23 24 25 26 27 28 29 2 3 4 5 6 7 8 9 NOP X
SScrofa11.1 description Pig (Sus scrofa) Release-97
SScrofa11.1 wget ftp://ftp.ensembl.org/pub/release-97/fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa.gz
SScrofa11.1 chromosome 1 18 X Y
Asagao1.2 description Asagao (Ipomoea nil) Japanese morning glory
Asagao1.2 wget http://viewer.shigen.info/asagao/data/Asagao_1.2.fa.gz
Asagao1.2 chromosome 0 0 10 11 12 13 14 15 1 2 3 4 5 6 7 8 9
SARS-CoV-2 description Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, NC_045512.2)
SARS-CoV-2 wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz
SARS-CoV-2 chromosome 0 0 NC_045512.2
Gifu1.2 description Lotus japonicus Gifu
Gifu1.2 wget http://viewer.shigen.info/lotus/data/Lj_Gifu_v1.2_genome.fa.gz
Gifu1.2 chromosome 0 0 1 2 3 4 5 6
HBV description Hepatitis B virus (strain ayw, NC_003977.2)
HBV wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/Hepatitis_B_virus/latest_assembly_versions/GCF_000861825.2_ViralProj15428/GCF_000861825.2_ViralProj15428_genomic.fna.gz
HBV chromosome 0 0 NC_003977.2
sacCer3 description Saccharomyces cerevisiae (UCSC sacCer3)
sacCer3 wget http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz
sacCer3 file S288C_reference_sequence_R64-1-1_20110203.fsa
sacCer3 chromosome 0 0 I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI NOP
Ecoli description Escherichia coli str. K-12 substr. MG1655 (NC_000913.3)
Ecoli wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gz
Ecoli chromosome 0 0 NC_000913.3
Bsubtilis description Bacillus subtilis subsp. subtilis str. 168 (NC_000913.3)
Bsubtilis wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/009/045/GCF_000009045.1_ASM904v1/GCF_000009045.1_ASM904v1_genomic.fna.gz
Bsubtilis chromosome 0 0 NC_000964.3
Vcholerae description Vibrio cholerae O1 biovar El Tor str. N16961
Vcholerae wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/745/GCF_000006745.1_ASM674v1/GCF_000006745.1_ASM674v1_genomic.fna.gz
Vcholerae chromosome 0 0 NC_002505.1 NC_002506.1
KOD1 description Thermococcus kodakarensis KOD1 (NC_006624.1)
KOD1 wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/009/965/GCF_000009965.1_ASM996v1/GCF_000009965.1_ASM996v1_genomic.fna.gz
KOD1 chromosome 0 0 NC_006624.1
RIB40 description Aspergillus oryzae RIB40 (ASM18445v3)
RIB40 wget ftp://ftp.ensemblgenomes.org/pub/fungi/release-47/fasta/aspergillus_oryzae/dna/Aspergillus_oryzae.ASM18445v3.dna.toplevel.fa.gz
RIB40 chromosome 0 0 NOP 1 2 3 4 5 6 7 8 AP007160 AP007177 AP007156
Camarosa1.0 description Strawberry (Fragaria x ananassa) Camarosa genome assembly v1.0
Camarosa1.0 wget https://www.rosaceae.org/rosaceae_downloads/Fragaria_x_ananassa/Fragaria_x_ananassa_Camarosa_Genome_v1.0.a1/assembly/F_ana_Camarosa_6-28-17.fasta.gz
Camarosa1.0 chromosome 0 0 1-1 1-2 1-3 1-4 2-1 2-2 2-3 2-4 3-1 3-2 3-3 3-4 4-1 4-2 4-3 4-4 5-1 5-2 5-3 5-4 6-1 6-2 6-3 6-4 7-1 7-2 7-3 7-4
Reikou2.3 description Strawberry Reikou genome v2.3
Reikou2.3 wget Access to http://strawberry-garden.kazusa.or.jp/cgi-bin/seqlist.cgi?db=FAN_r2.3&ext=genome > Download > FAN_r2.3 > FAN_r2.3.chr1-7.fasta.gz Save FAN_r2.3.chr1-7.fasta.gz into Reikou2.3 directory
Reikou2.3 file FAN_r2.3.chr1-7.fasta.gz
Reikou2.3 chromosome 0 0 1Ava 1Avb 1Bia 1Bib 1X1a 1X1b 1X2a 1X2b 1X3a 1X3b 2Ava 2Avb 2Bia 2Bib 2X1a 2X1b 2X2a 2X2b 3Ava 3Avb 3Bia 3Bib 3X1a 3X1b 3X2a 3X2b 4Ava 4Avb 4Bia 4Bib 4X1a 4X1b 4X2a 4X2b 5Ava 5Avb 5Bia 5Bib 5X1a 5X1b 5X2a 5X2b 6Av1a 6Av1b 6Av2a 6Av2b 6Bia 6Bib 6X1a 6X1b 6X2a 6X2b 6X3a 6X3b 7Ava 7Avb 7Bia 7Bib 7X1a 7X1b 7X2a 7X2b
97103 description Water melon (Citrullus lanatus subsp. vulgaris) cv. 97213v2
97103 wget http://cucurbitgenomics.org/ftp/genome/watermelon/97103/v2/97103_genome_v2.fa.gz
97103 chromosome 1 11
CharlestonGray2 description Water melon (Citrullus lanatus subsp. vulgaris) cv. Charleston Gray v2
CharlestonGray2 wget http://cucurbitgenomics.org/ftp/genome/watermelon/WCG/v2/WCG_genome_v2.fa.gz
CharlestonGray2 chromosome 1 11
Camellia20200506 description Black tea (Cammellia sinensis) assembly
Camellia20200506 wget Access to http://tpdb.shengxin.ren/; Download CSS_ChrLev_20200506_Genome.fas.gz; Save the gz file into Camellia20200506 directory; And then run ped.pl.
Camellia20200506 file CSS_ChrLev_20200506_Genome.fas.gz
CsinensisHz2 description Sweet orange (Citrus sinensis) Hzau v2.0
CsinensisHz2 wget https://www.citrusgenomedb.org/citrus_downloads/Citrus_sinensis/C.sinensis_Hzau_v2.0_genome/assembly/C.sinensis_v2.0_HZAU_csi.chromosome.masked.fa
CsinensisHz2 chromosome 1 9