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nikellepetrillo merged 9 commits into from
Feb 19, 2026
Merged

Np add 5 new references to BuildIndices documentation #1776

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988c8bf
dummy commit
nikellepetrillo Jan 27, 2026
c44ab80
Merge remote-tracking branch 'origin/develop' into develop
nikellepetrillo Feb 5, 2026
a4515e0
Merge remote-tracking branch 'origin/develop' into develop
nikellepetrillo Feb 10, 2026
8f16317
Merge remote-tracking branch 'origin/develop' into develop
nikellepetrillo Feb 18, 2026
f73c940
add owl monkey, lemur, and mole rat to docs
nikellepetrillo Feb 18, 2026
e8ff537
add owl monkey, lemur, and mole rat to docs
nikellepetrillo Feb 18, 2026
c2567c7
update example input jsons
nikellepetrillo Feb 18, 2026
9a35fb0
add chimp and ferret
nikellepetrillo Feb 18, 2026
8e2c0ca
add treeshrew
nikellepetrillo Feb 19, 2026
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2 changes: 1 addition & 1 deletion pipelines/wdl/build_indices/Chimp.json
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Expand Up @@ -10,5 +10,5 @@
"BuildIndices.mito_ref_gbk": "gs://fc-secure-aae9980f-2d1b-4f56-ab67-3968a0f95aef/chimp/sequence.gb",
"BuildIndices.organism": "Chimp",
"BuildIndices.run_mitofinder": "true",
"BuildIndices.skip_gtf_modification": "true"
"BuildIndices.run_modify_gtf": "false"
}
2 changes: 1 addition & 1 deletion pipelines/wdl/build_indices/Ferret.json
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"BuildIndices.mito_ref_gbk": "gs://fc-secure-aae9980f-2d1b-4f56-ab67-3968a0f95aef/Ferret/sequence.gb",
"BuildIndices.organism": "Ferret",
"BuildIndices.run_mitofinder": "true",
"BuildIndices.skip_gtf_modification": "true"
"BuildIndices.run_modify_gtf": "false"
}
2 changes: 1 addition & 1 deletion pipelines/wdl/build_indices/GrayMouseLemur.json
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"BuildIndices.mito_ref_gbk": "gs://fc-secure-aae9980f-2d1b-4f56-ab67-3968a0f95aef/gray_mouse_lemur/sequence.gb",
"BuildIndices.organism": "Gray_mouse_lemur",
"BuildIndices.run_mitofinder": "true",
"BuildIndices.skip_gtf_modification": "true"
"BuildIndices.run_modify_gtf": "false"
}
2 changes: 1 addition & 1 deletion pipelines/wdl/build_indices/NakedMoleRat.json
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"BuildIndices.mito_ref_gbk": "gs://fc-secure-aae9980f-2d1b-4f56-ab67-3968a0f95aef/naked_mole_rat/sequence.gb",
"BuildIndices.organism": "Naked_mole_rat",
"BuildIndices.run_mitofinder": "true",
"BuildIndices.skip_gtf_modification": "true"
"BuildIndices.run_modify_gtf": "false"
}
2 changes: 1 addition & 1 deletion pipelines/wdl/build_indices/OwlMonkey.json
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"BuildIndices.mito_ref_gbk": "gs://fc-secure-aae9980f-2d1b-4f56-ab67-3968a0f95aef/Ferret/sequence.gb",
"BuildIndices.organism": "Owl_monkey",
"BuildIndices.run_mitofinder": "true",
"BuildIndices.skip_gtf_modification": "true"
"BuildIndices.run_modify_gtf": "false"
}
55 changes: 55 additions & 0 deletions website/docs/Pipelines/BuildIndices_Pipeline/README.md
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Expand Up @@ -248,6 +248,61 @@ Marmoset scripts expect a custom-modified input Marmoset GTF file. These inputs
| STAR Index TAR | `gs://gcp-public-data--broad-references/S.scrofa/Sscrofa11.1/cleanome/star/v2_7_10a/modified_star2.7.10a-Pig-NCBI-build-Sscrofa11.1-2.2.tar` |
| GTF Annotation | `gs://gcp-public-data--broad-references/S.scrofa/Sscrofa11.1/cleanome/star/v2_7_10a/modified_v2.2.annotation.gtf` |

### Owl Monkey
| File Type | File Location |
|---------------------|--------------|
| Genomic Reference | 86718_ANA_hifiasm-v0.15.2.pri (NCBI) |
| Gene Annotation | RefSeq GCF_030222135.1 |
| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/A.nancymaae/86718_ANA_hifiasm-v0.15.2.pri/cleanome/bwa/v2_2_1/bwa-mem2-2.2.1-Owl_monkey-NCBI-build-86718_ANA_hifiasm-v0.15.2.pri.tar` |
| Chromosome Sizes | `gs://gcp-public-data--broad-references/A.nancymaae/86718_ANA_hifiasm-v0.15.2.pri/cleanome/bwa/v2_2_1/chrom.sizes` |
| STAR Index TAR | `gs://gcp-public-data--broad-references/A.nancymaae/86718_ANA_hifiasm-v0.15.2.pri/cleanome/star/v2_7_10a/star2.7.10a-Owl_monkey-NCBI-build-86718_ANA_hifiasm-v0.15.2.pri-GCF_030222135.1.tar` |
| GTF Annotation | `gs://gcp-public-data--broad-references/A.nancymaae/86718_ANA_hifiasm-v0.15.2.pri/cleanome/star/v2_7_10a/vGCF_030222135.1.annotation.gtf` |
| MT Genes List | `gs://gcp-public-data--broad-references/A.nancymaae/86718_ANA_hifiasm-v0.15.2.pri/cleanome/owl_monkey_mt_genes_list.txt` |

### Lemur
| File Type | File Location |
|---------------------|--------------|
| Genomic Reference | Mmur_3.0 (NCBI) |
| Gene Annotation | RefSeq GCF_000165445.2 |
| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/M.murinus/Mmur_3.0/cleanome/bwa/v2_2_1/bwa-mem2-2.2.1-Gray_mouse_lemur-NCBI-build-Mmur_3.0.tar` |
| Chromosome Sizes | `gs://gcp-public-data--broad-references/M.murinus/Mmur_3.0/cleanome/bwa/v2_2_1/chrom.sizes` |
| STAR Index TAR | `gs://gcp-public-data--broad-references/M.murinus/Mmur_3.0/cleanome/star/v2_7_10a/star2.7.10a-Gray_mouse_lemur-NCBI-build-Mmur_3.0-GCF_000165445.2.tar` |
| GTF Annotation | `gs://gcp-public-data--broad-references/M.murinus/Mmur_3.0/cleanome/star/v2_7_10a/vGCF_000165445.2.annotation.gtf` |
| MT Genes List | `gs://gcp-public-data--broad-references/M.murinus/Mmur_3.0/cleanome/lemur_mt_genes_list.txt` |

### Naked Mole Rat
| File Type | File Location |
|---------------------|--------------|
| Genomic Reference | HetGla_female_1.0 (NCBI) |
| Gene Annotation | RefSeq GCF_000247695.1 |
| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/H.glaber/HetGla_female_1.0/cleanome/bwa/bwa-mem2-2.2.1-Naked_mole_rat-NCBI-build-HetGla_female_1.0.tar` |
| Chromosome Sizes | `gs://gcp-public-data--broad-references/H.glaber/HetGla_female_1.0/cleanome/bwa/chrom.sizes` |
| STAR Index TAR | `gs://gcp-public-data--broad-references/H.glaber/HetGla_female_1.0/cleanome/star/v2_7_10a/star2.7.10a-Naked_mole_rat-NCBI-build-HetGla_female_1.0-GCF_000247695.1.tar` |
| GTF Annotation | `gs://gcp-public-data--broad-references/H.glaber/HetGla_female_1.0/cleanome/star/v2_7_10a/vGCF_000247695.1.annotation.gtf` |
| MT Genes List | `gs://gcp-public-data--broad-references/H.glaber/HetGla_female_1.0/cleanome/naked_mole_rat_mt_genes_list.txt` |

### Chimp
| File Type | File Location |
|---------------------|--------------|
| Genomic Reference | NHGRI_mPanTro3-v2.0_pri (NCBI) |
| Gene Annotation | RefSeq GCF_028858775.2 |
| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/P.troglodytes/NHGRI_mPanTro3-v2.0_pri/cleanome/bwa/v2_2_1/bwa-mem2-2.2.1-Chimp-NCBI-build-NHGRI_mPanTro3-v2.0_pri.tar` |
| Chromosome Sizes | `gs://gcp-public-data--broad-references/P.troglodytes/NHGRI_mPanTro3-v2.0_pri/cleanome/bwa/v2_2_1/chrom.sizes` |
| STAR Index TAR | `gs://gcp-public-data--broad-references/P.troglodytes/NHGRI_mPanTro3-v2.0_pri/cleanome/star/v2_7_10a/star2.7.10a-Chimp-NCBI-build-NHGRI_mPanTro3-v2.0_pri-GCF_028858775.2.tar` |
| GTF Annotation | `gs://gcp-public-data--broad-references/P.troglodytes/NHGRI_mPanTro3-v2.0_pri/cleanome/star/v2_7_10a/vGCF_028858775.2.annotation.gtf` |
| MT Genes List | `gs://gcp-public-data--broad-references/P.troglodytes/NHGRI_mPanTro3-v2.0_pri/cleanome/chimp_mt_genes_list.txt` |

### Ferret
| File Type | File Location |
|---------------------|--------------|
| Genomic Reference | ASM1176430v1.1 (NCBI) |
| Gene Annotation | RefSeq GCF_011764305.1 |
| BWA-MEM2 Index TAR | `gs://gcp-public-data--broad-references/M.putorius_furo/ASM1176430v1.1/cleanome/bwa/v2_2_1/bwa-mem2-2.2.1-Ferret-NCBI-build-ASM1176430v1.1.tar` |
| Chromosome Sizes | `gs://gcp-public-data--broad-references/M.putorius_furo/ASM1176430v1.1/cleanome/bwa/v2_2_1/chrom.sizes` |
| STAR Index TAR | `gs://gcp-public-data--broad-references/M.putorius_furo/ASM1176430v1.1/cleanome/star/v2_7_10a/star2.7.10a-Ferret-NCBI-build-ASM1176430v1.1-GCF_011764305.1.tar` |
| GTF Annotation | `gs://gcp-public-data--broad-references/M.putorius_furo/ASM1176430v1.1/cleanome/star/v2_7_10a/vGCF_011764305.1.annotation.gtf` |
| MT Genes List | `gs://gcp-public-data--broad-references/M.putorius_furo/ASM1176430v1.1/cleanome/ferret_mt_genes_list.txt` |

### Viral references

| Species | Species reference | Species annotation | Viral reference | Viral annotation |
Expand Down
10 changes: 4 additions & 6 deletions website/docs/Pipelines/BuildIndices_Pipeline/ReferencesSpecies.md
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Expand Up @@ -13,14 +13,12 @@ The following table lists species for which reference files have been built or a
|Macaque|Macaca mulatta|mmul10|[RefSeq annotation version 103](https://www.google.com/url?source=gmail&sa=E&q=https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Macaca_mulatta/103/)|Production|
|Marmoset|Callithrix jacchus|mCalJa1.2.pat.X (GenBank Accession GCA_011100555.2 and RefSeq Accession GCF_011100555.1)|Custom GTF with mitochondrial chromosomes|Production|
|Armadillo (Nine-banded)|Dasypus novemcinctus|mDasNov1.hap2 (NCBI)|RefSeq GCF_030445035.1-RS_2023_07|Available|
|Ferret|Mustela putorius furo|ASM1176430v1.1 (NCBI)|GCF_011764305.1 (NCBI)|Coming Soon|
|Galago|Otolemur garnettii|OtoGar3 (NCBI)|GCF_000181295.1 (NCBI)|Coming Soon|
|Mouse lemur|Microcebus murinus|Mmur_3.0 (NCBI)|GCF_000165445.2 (NCBI)|Coming Soon|
|Ferret|Mustela putorius furo|ASM1176430v1.1 (NCBI)|GCF_011764305.1 (NCBI)|Available|
|Mouse lemur|Microcebus murinus|Mmur_3.0 (NCBI)|GCF_000165445.2 (NCBI)|Available|
|Naked mole rat|Heterocephalus glaber|HetGla_female_1.0 (NCBI)|GCF_000247695.1 (NCBI)|Available|
|Opossum|Monodelphis domestica|mMonDom1.pri (NCBI)|RefSeq GCF_027887165.1-RS_2023_05|Available|
|Owl monkey|Aotus nancymaae|86718_ANA_hifiasm-v0.15.2.pri (NCBI)|GCF_030222135.1 (NCBI)|Coming Soon|
|Owl monkey|Aotus nancymaae|86718_ANA_hifiasm-v0.15.2.pri (NCBI)|GCF_030222135.1 (NCBI)|Available|
|Pig|Sus scrofa|Sscrofa11.1 (NCBI)|NCBI Annotation Release 106 (RefSeq GCF_000003025.6_Sscrofa11.1)|Available|
|Rat|Rattus norvegicus|mRatBN7.2 (NCBI)|RefSeq GCF_015227675.2-RS_2023_06|Available|
|Treeshrew|Tupaia belangeri|TupChi_1.0 (NCBI)|GCF_000334495.1 (NCBI)|Coming Soon|
|Chimpanzee|Pan troglodytes|NHGRI_mPanTro3-v2.0_pri (NCBI)|GCF_028858775.2 (NCBI)|Coming Soon|
|Harbor porpoise|Phocoena phocoena|mPhoSin1.pri (NCBI)|GCF_008692025.1 (NCBI)|Coming Soon|
|Chimpanzee|Pan troglodytes|NHGRI_mPanTro3-v2.0_pri (NCBI)|GCF_028858775.2 (NCBI)|Available|