config

#
# 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

Lactuca_sativa	description	Lettuce (Lactuca sativa)
Lactuca_sativa	wget	ftp://ftp.ncbi.nlm.nih.gov/genomes/.vol2/all/GCA/002/870/075/GCA_002870075.4_Lsat_Salinas_v11/GCA_002870075.4_Lsat_Salinas_v11_genomic.fna.gz
Lactuca_sativa	chromosome	1	9