cfd801899529a9a9b0db3cc408a8f5e3c6ecb670 hiram Thu May 15 13:24:49 2025 -0700 implement a scientific name override system to fixup names for F1 hybrid diploid assemblies refsd #34917 diff --git src/hg/makeDb/doc/asmHubs/sciNameOverride.txt src/hg/makeDb/doc/asmHubs/sciNameOverride.txt new file mode 100644 index 00000000000..fe019e974c7 --- /dev/null +++ src/hg/makeDb/doc/asmHubs/sciNameOverride.txt @@ -0,0 +1,22 @@ +# override table for F1 cross hybrid assemblies where both haplotypes +# are individual assemblies. Each individual assembly should have the +# correct scientific species name (and subsequent) taxId for the actual +# genome that it represents +GCA_015852565.1 GCA_015852565.1_bf_hap-2 Branchiostoma floridae 7739 +GCA_019207075.1 GCA_019207075.1_Bb-hap Branchiostoma belcheri 7741 +GCF_003369695.1 GCF_003369695.1_UOA_Brahman_1 Bos indicus 9915 +GCA_003369685.2 GCA_003369685.2_UOA_Angus_1 Bos taurus 9913 + + +# invertebrateAsmHub/invertebrate.orderList.tsv:GCA_019207075.1_Bb-hap lancelets B.floridae x B.belcheri (bbbf 2021) +# invertebrateAsmHub/invertebrate.orderList.tsv:GCA_015852565.1_bf_hap-2 lancelets B.floridae x B.japonicum (bjbf 2020) +# invertebrateAsmHub/invertebrate.orderList.tsv:GCF_000209225.1_ASM20922v1 starlet sea anemone (CH2 x CH6 2007 JGI) +# mammalsAsmHub/mammals.orderList.tsv:GCA_003369685.2_UOA_Angus_1 hybrid cattle (Angus x Brahman F1 Angus haplotype 2018) +# mammalsAsmHub/mammals.orderList.tsv:GCF_003369695.1_UOA_Brahman_1 hybrid cattle (Angus x Brahman F1 Brahman haplotype 2018) +# mammalsAsmHub/mammals.orderList.tsv:GCF_029378745.1_NIAB-ARS_B.indTharparkar_mat_pri_1.0 zebu cattle (Sahiwal x Tharparkar maternal NIAB-ARS_2022 2023) +# plantsAsmHub/plants.orderList.tsv:GCA_946000675.1_VITVix101-14Mgt_v1.0 eudicot V.riparia x Vitis rupestris (2022) +# plantsAsmHub/plants.orderList.tsv:GCF_004785595.1_Jm3101_v1.0 J.microcarpa x regia eudicots (UCDavis 2019) +# vgpAsmHub/vgp.alternate.orderList.tsv:GCA_003369685.2_UOA_Angus_1 hybrid cattle (Angus x Brahman F1 Angus haplotype 2018) +# vgpAsmHub/vgp.primary.orderList.tsv:GCF_003369695.1_UOA_Brahman_1 hybrid cattle (Angus x Brahman F1 Brahman haplotype 2018) +# vgpAsmHub/vgp.primary.orderList.tsv:GCA_019207075.1_Bb-hap lancelets B.floridae x B.belcheri (bbbf 2021) +# vgpAsmHub/vgp.primary.orderList.tsv:GCA_015852565.1_bf_hap-2 lancelets B.floridae x B.japonicum (bjbf 2020)