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Merged
ahernank merged 4 commits into from
Apr 24, 2026
Merged

Incorrect text in several VUGs #129

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9a58167
Updated VUGs
jonbrenas Mar 15, 2026
8e1373a
Corrected typo
jonbrenas Mar 15, 2026
f8133e3
Removing adds and adding literature sample sets
jonbrenas Apr 7, 2026
256808c
Missed a few changes
jonbrenas Apr 7, 2026
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14 changes: 10 additions & 4 deletions docs/af1/af1.1.ipynb
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Expand Up @@ -54,7 +54,13 @@
"- [1315-VO-NG-OMITOLA](https://www.malariagen.net/network/where-we-work/1315-VO-NG-OMITOLA) - ANOSPP screening of _Anopheles_ species and _Plasmodium_ presence in malaria vectors in Nigeria\n",
"- [1326-VO-UG-KAYONDO](https://www.malariagen.net/network/where-we-work/1326-VO-UG-KAYONDO) - ANOSPP screening of _Anopheles_ species and _Plasmodium_ presence in malaria vectors in Uganda\n",
"\n",
"This release also includes data from one study openly available in the literature: [small-2020-af](https://doi.org/10.1073/pnas.2018142117), and samples from studies ([AG1000G-KE](https://www.malariagen.net/network/where-we-work/ag1000g-ke), [AG1000G-MW](https://www.malariagen.net/network/where-we-work/ag1000g-mw), [AG1000G-TZ](https://www.malariagen.net/network/where-we-work/ag1000g-tz)) part of the [Ag3.0 (Ag1000G phase 3)](https://malariagen.github.io/vector-data/ag3/ag3.0.html) project, which were identified as _Anopheles_ funestus.\n",
"This release also includes data from one study openly available in the literature:\n",
"- small-2020-af - [Radiation with reticulation marks the origin of a major malaria vector](https://doi.org/10.1073/pnas.2018142117)\n",
"\n",
"This release also includes samples which were identified as _Anopheles_ funestus from the following studies which are part of the [Ag3.0 (Ag1000G phase 3)](https://malariagen.github.io/vector-data/ag3/ag3.0.html) project: \n",
"- [AG1000G-KE](https://www.malariagen.net/network/where-we-work/ag1000g-ke)\n",
"- [AG1000G-MW](https://www.malariagen.net/network/where-we-work/ag1000g-mw)\n",
"- [AG1000G-TZ](https://www.malariagen.net/network/where-we-work/ag1000g-tz)\n",
"\n",
"\n",
"For full details on the studies in Ag1000G please visit the [Ag1000G partner studies guide](https://malariagen.github.io/vector-data/studies-ag1000g.html)."
Expand All @@ -68,7 +74,7 @@
"source": [
"## Whole-genome sequencing and variant calling\n",
"\n",
"All samples in `Af1.1` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. "
"Most samples in `Af1.1` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. Exceptions are samples in `1236-VO-TZ-OKUMU-VMF00248` which have been sequenced individually to high coverage by a commercial provider, and samples in `small-2020-af` which have been curated from the literature ([small-2020-af](https://doi.org/10.1073/pnas.2018142117)). These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. "
]
},
{
Expand Down Expand Up @@ -1256,9 +1262,9 @@
},
"environment": {
"kernel": "mgenv_7.2.0",
"name": "workbench-notebooks.m138",
"name": "workbench-notebooks.m139",
"type": "gcloud",
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138"
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139"
},
"kernelspec": {
"display_name": "Python (mgenv_7.2.0)",
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9 changes: 5 additions & 4 deletions docs/af1/af1.2.ipynb
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Expand Up @@ -46,7 +46,8 @@
"\n",
"- [1281-VO-CM-CHRISTOPHE](https://www.malariagen.net/network/where-we-work/1281-VO-CM-CHRISTOPHE) - PAMCA _Anopheles_ genomics programme - Malaria vector surveillance, population genetics and insecticide resistance characterization in four eco-epidemiological settings in Cameroon\n",
"\n",
"This release also includes data from one study openly available in the literature: [small-2023](https://doi.org/10.1073/pnas.2219835120)"
"This release also includes data from one study openly available in the literature:\n",
"- small-2023 - [Standing genetic variation and chromosome differences drove rapid ecotype formation in a major malaria mosquito](https://doi.org/10.1073/pnas.2219835120)"
]
},
{
Expand All @@ -57,7 +58,7 @@
"source": [
"## Whole-genome sequencing and variant calling\n",
"\n",
"All samples in `Af1.2` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. "
"All samples in 1281-VO-CM-CHRISTOPHE-VMF00227 have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute, all samples in `1236-VO-TZ-OKUMU-VMF00252` have been sequenced individually to high coverage by a commercial provider, and all samples in `small-2020-af` have been curated from the literature ([small-2023](https://doi.org/10.1073/pnas.2219835120)). These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. "
]
},
{
Expand Down Expand Up @@ -685,9 +686,9 @@
},
"environment": {
"kernel": "mgenv_7.2.0",
"name": "workbench-notebooks.m138",
"name": "workbench-notebooks.m139",
"type": "gcloud",
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138"
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139"
},
"kernelspec": {
"display_name": "Python (mgenv_7.2.0)",
Expand Down
6 changes: 3 additions & 3 deletions docs/af1/af1.3.ipynb
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Expand Up @@ -53,7 +53,7 @@
"source": [
"## Whole-genome sequencing and variant calling\n",
"\n",
"All samples in `Af1.3` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. "
"All samples in `Af1.3` have been sequenced individually to high coverage by a commercial provider. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. "
]
},
{
Expand Down Expand Up @@ -648,9 +648,9 @@
},
"environment": {
"kernel": "mgenv_7.2.0",
"name": "workbench-notebooks.m138",
"name": "workbench-notebooks.m139",
"type": "gcloud",
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138"
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139"
},
"kernelspec": {
"display_name": "Python (mgenv_7.2.0)",
Expand Down
6 changes: 3 additions & 3 deletions docs/af1/af1.4.ipynb
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Expand Up @@ -57,7 +57,7 @@
"source": [
"## Whole-genome sequencing and variant calling\n",
"\n",
"All samples in `Af1.4` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. "
"Most samples in `Af1.4` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. Exceptions are samples in 1354-VO-KE-DONNELLY-VMF00281 which have been sequenced individually to high coverage by a commercial provider. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. "
]
},
{
Expand Down Expand Up @@ -685,9 +685,9 @@
},
"environment": {
"kernel": "mgenv_7.2.0",
"name": "workbench-notebooks.m138",
"name": "workbench-notebooks.m139",
"type": "gcloud",
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138"
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139"
},
"kernelspec": {
"display_name": "Python (mgenv_7.2.0)",
Expand Down
14 changes: 10 additions & 4 deletions docs/ag3/ag3.10.ipynb
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Expand Up @@ -58,7 +58,7 @@
"source": [
"## Whole-genome sequencing and variant calling\n",
"\n",
"All samples in `Ag3.10` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. \n",
"Most samples in `Ag3.10` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. Exceptions are samples in `fontaine-2015-rebuild` which have been curated from the literature ([fontaine-2015-rebuild](https://doi.org/10.1126/science.1258524)). These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. \n",
"\n",
"\n",
"For further information about the sequencing and variant calling methods used, please see the [methods page](methods)."
Expand Down Expand Up @@ -1035,10 +1035,16 @@
"name": "Ag3.0-intro.ipynb",
"provenance": []
},
"environment": {
"kernel": "mgenv_7.2.0",
"name": "workbench-notebooks.m139",
"type": "gcloud",
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139"
},
"kernelspec": {
"display_name": "global-global-mgenv-6.0.6",
"display_name": "Python (mgenv_7.2.0)",
"language": "python",
"name": "conda-env-global-global-mgenv-6.0.6-py"
"name": "mgenv_7.2.0"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -1050,7 +1056,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.12.11"
}
},
"nbformat": 4,
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16 changes: 11 additions & 5 deletions docs/ag3/ag3.7.ipynb
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Expand Up @@ -48,7 +48,7 @@
"- [1270-VO-MULTI-PAMGEN](https://www.malariagen.net/network/where-we-work/1270-VO-MULTI-PAMGEN) - _Pan-African Malaria Genetic Epidemiology Network (PAMGEN) Anopheles gambiae samples (Cameroon)_\n",
"- [1281-VO-CM-CHRISTOPHE](https://www.malariagen.net/network/where-we-work/1281-VO-CM-CHRISTOPHE) - _PAMCA Anopheles genomics programme - Malaria vector surveillance, population genetics and insecticide resistance characterization in four eco-epidemiological settings in Cameroon_\n",
"\n",
"This release also includes data from 2 studies openly available in the literature: [barron-2019](https://doi.org/10.1038/s41598-019-49065-5) and [crawford-2016](https://doi.org/10.1111/mec.13572)."
"This release also includes data from 2 studies openly available in the literature: [_A new species in the major malaria vector complex sheds light on reticulated species evolution_](https://doi.org/10.1038/s41598-019-49065-5) and [_Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae s.l., and its impact on susceptibility to Plasmodium infection_](https://doi.org/10.1111/mec.13572)."
]
},
{
Expand All @@ -59,7 +59,7 @@
"source": [
"## Whole-genome sequencing and variant calling\n",
"\n",
"All samples in `Ag3.7` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. \n",
"Most samples in `Ag3.7` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. Exceptions are samples in `crawford-2016` and `barron-2019` which have been curated from the literature ([crawford-2016](https://doi.org/10.1111/mec.13572) and [barron-2019](https://doi.org/10.1038/s41598-019-49065-5)). These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. \n",
"\n",
"\n",
"For further information about the sequencing and variant calling methods used, please see the [methods page](methods)."
Expand Down Expand Up @@ -948,10 +948,16 @@
"name": "Ag3.0-intro.ipynb",
"provenance": []
},
"environment": {
"kernel": "mgenv_7.2.0",
"name": "workbench-notebooks.m139",
"type": "gcloud",
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139"
},
"kernelspec": {
"display_name": "global-global-mgenv-6.0.6",
"display_name": "Python (mgenv_7.2.0)",
"language": "python",
"name": "conda-env-global-global-mgenv-6.0.6-py"
"name": "mgenv_7.2.0"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -963,7 +969,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.12.11"
}
},
"nbformat": 4,
Expand Down
17 changes: 12 additions & 5 deletions docs/ag3/ag3.8.ipynb
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Expand Up @@ -48,7 +48,8 @@
"- [1315-VO-NG-OMITOLA](https://www.malariagen.net/network/where-we-work/1315-VO-NG-OMITOLA) - _ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in Nigeria_\n",
"- [1326-VO-UG-KAYONDO](https://www.malariagen.net/network/where-we-work/1326-VO-UG-KAYONDO) - _ANOSPP screening of Anopheles species and Plasmodium presence in malaria vectors in Uganda_\n",
"\n",
"This release also includes data from one study openly available in the literature: [tennessen-2021](https://doi.org/10.1111/mec.15756)."
"This release also includes data from one study openly available in the literature: \n",
"- tennessen-2021 - [_A population genomic unveiling of a new cryptic mosquito taxon within the malaria-transmitting Anopheles gambiae complex_](https://doi.org/10.1111/mec.15756)."
]
},
{
Expand All @@ -59,7 +60,7 @@
"source": [
"## Whole-genome sequencing and variant calling\n",
"\n",
"All samples in `Ag3.8` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. \n",
"Most samples in `Ag3.8` have been sequenced individually to high coverage using Illumina technology at the Wellcome Sanger Institute. Exceptions are samples in `tennessen-2021` which have been curated from the literature ([tennessen-2021](https://doi.org/10.1111/mec.15756)). These sequence data have then been analysed to identify genetic variants such as single nucleotide polymorphisms (SNPs). After variant calling, both the samples and the variants have been through a range of quality control analyses, to ensure the data are of high quality. Both the raw sequence data and the curated variant calls are openly available for download and analysis. \n",
"\n",
"\n",
"For further information about the sequencing and variant calling methods used, please see the [methods page](methods)."
Expand Down Expand Up @@ -964,10 +965,16 @@
"name": "Ag3.0-intro.ipynb",
"provenance": []
},
"environment": {
"kernel": "mgenv_7.2.0",
"name": "workbench-notebooks.m139",
"type": "gcloud",
"uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m139"
},
"kernelspec": {
"display_name": "global-global-mgenv-6.0.6",
"display_name": "Python (mgenv_7.2.0)",
"language": "python",
"name": "conda-env-global-global-mgenv-6.0.6-py"
"name": "mgenv_7.2.0"
},
"language_info": {
"codemirror_mode": {
Expand All @@ -979,7 +986,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.12.11"
}
},
"nbformat": 4,
Expand Down
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