From 3271be81cc3aff6b40cb921586ec498c18e7c8d7 Mon Sep 17 00:00:00 2001 From: marcel-keller <61977721+marcel-keller@users.noreply.github.com> Date: Mon, 9 Dec 2024 16:32:37 +0100 Subject: [PATCH 1/3] Update ancientsinglegenome-hostassociated_libraries.tsv Bonczarowska2023 is half-UDG data and not non-UDG, as stated in the previous version. --- .../ancientsinglegenome-hostassociated_libraries.tsv | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index e2e5967e..aa9bd3e0 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -2817,11 +2817,11 @@ Neumann2023 2023 10.1553/archaeologia107 DSH025 ENA PRJEB61070 ERS15547238 DSH02 Neumann2023 2023 10.1553/archaeologia107 DSH008 ENA PRJEB61070 ERS15547237 DSH008.A0201.YP1.1 single AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE Targeted-Capture 6850253 ERR11479452 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/052/ERR11479452/ERR11479452.fastq.gz 869fdf1366e7bceba885863135667f7d 205976513 Neumann2023 2023 10.1553/archaeologia107 DSH008 ENA PRJEB61070 ERS15547235 DSH008.A0101.SG1.1 single AccuPrime Pfx DNA none Illumina HiSeq 4000 SINGLE WGS 3973592 ERR11479449 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/049/ERR11479449/ERR11479449.fastq.gz 6cf53899d806b5373b9846c9cffbebc7 124500605 Neumann2023 2023 10.1553/archaeologia107 DSH025 ENA PRJEB61070 ERS15547236 DSH025.A0101.SG1.1 single AccuPrime Pfx DNA none Illumina HiSeq 4000 SINGLE WGS 4901176 ERR11479450 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/050/ERR11479450/ERR11479450.fastq.gz 999057c65a6ca3edeef32cbb714645ab 143481817 -Bonczarowska2023 2023 10.1098/rspb.2023.0622 X52 ENA PRJEB60595 ERS14773586 X52T double PfuTurbo Cx Hotstart DNA none Illumina NovaSeq 6000 PAIRED WGS 1292846992 ERR11478695 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/095/ERR11478695/ERR11478695_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/095/ERR11478695/ERR11478695_2.fastq.gz f253781a551cdf2415c9381715a3bcee;a392e90f10a7b28677870ece699773f5 29915422152;31546072181 -Bonczarowska2023 2023 10.1098/rspb.2023.0622 X3003 ENA PRJEB60595 ERS14773585 X3003T double PfuTurbo Cx Hotstart DNA none Illumina NovaSeq 6000 PAIRED WGS 20632842 ERR11011327 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/027/ERR11011327/ERR11011327_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/027/ERR11011327/ERR11011327_2.fastq.gz a4a298f0a640223c6ec99d7f3855adc2;6586c9bba9ceda8ab6359fa94980c743 467638929;445341650 -Bonczarowska2023 2023 10.1098/rspb.2023.0622 X52 ENA PRJEB60595 ERS14773586 X52T_3 double PfuTurbo Cx Hotstart DNA none Illumina NovaSeq 6000 PAIRED WGS 21145732 ERR11011329 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/029/ERR11011329/ERR11011329_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/029/ERR11011329/ERR11011329_2.fastq.gz 7642790292dc433986c6159b2d708b99;d3ca94b15ab06613149b702f45882089 471808218;493240187 -Bonczarowska2023 2023 10.1098/rspb.2023.0622 X3003 ENA PRJEB60595 ERS14773585 X3003T_2 double PfuTurbo Cx Hotstart DNA none Illumina NovaSeq 6000 PAIRED WGS 229864836 ERR11011330 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/030/ERR11011330/ERR11011330_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/030/ERR11011330/ERR11011330_2.fastq.gz 5937f8e01e4a0c32e0059cd506432f2e;23d59102b0dfb3a5722ec08dc1b5a5cc 4985082432;5107020039 -Bonczarowska2023 2023 10.1098/rspb.2023.0622 X52 ENA PRJEB60595 ERS14773586 X52T_2 double PfuTurbo Cx Hotstart DNA none Illumina NovaSeq 6000 PAIRED WGS 1329592756 ERR11435697 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/097/ERR11435697/ERR11435697_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/097/ERR11435697/ERR11435697_2.fastq.gz ae96523cb62dbd7cd7c27530039eff97;7617998ef105698c866d6cdedf8710ea 30549343594;29093388600 +Bonczarowska2023 2023 10.1098/rspb.2023.0622 X52 ENA PRJEB60595 ERS14773586 X52T double PfuTurbo Cx Hotstart DNA half-udg Illumina NovaSeq 6000 PAIRED WGS 1292846992 ERR11478695 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/095/ERR11478695/ERR11478695_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/095/ERR11478695/ERR11478695_2.fastq.gz f253781a551cdf2415c9381715a3bcee;a392e90f10a7b28677870ece699773f5 29915422152;31546072181 +Bonczarowska2023 2023 10.1098/rspb.2023.0622 X3003 ENA PRJEB60595 ERS14773585 X3003T double PfuTurbo Cx Hotstart DNA half-udg Illumina NovaSeq 6000 PAIRED WGS 20632842 ERR11011327 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/027/ERR11011327/ERR11011327_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/027/ERR11011327/ERR11011327_2.fastq.gz a4a298f0a640223c6ec99d7f3855adc2;6586c9bba9ceda8ab6359fa94980c743 467638929;445341650 +Bonczarowska2023 2023 10.1098/rspb.2023.0622 X52 ENA PRJEB60595 ERS14773586 X52T_3 double PfuTurbo Cx Hotstart DNA half-udg Illumina NovaSeq 6000 PAIRED WGS 21145732 ERR11011329 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/029/ERR11011329/ERR11011329_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/029/ERR11011329/ERR11011329_2.fastq.gz 7642790292dc433986c6159b2d708b99;d3ca94b15ab06613149b702f45882089 471808218;493240187 +Bonczarowska2023 2023 10.1098/rspb.2023.0622 X3003 ENA PRJEB60595 ERS14773585 X3003T_2 double PfuTurbo Cx Hotstart DNA half-udg Illumina NovaSeq 6000 PAIRED WGS 229864836 ERR11011330 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/030/ERR11011330/ERR11011330_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR110/030/ERR11011330/ERR11011330_2.fastq.gz 5937f8e01e4a0c32e0059cd506432f2e;23d59102b0dfb3a5722ec08dc1b5a5cc 4985082432;5107020039 +Bonczarowska2023 2023 10.1098/rspb.2023.0622 X52 ENA PRJEB60595 ERS14773586 X52T_2 double PfuTurbo Cx Hotstart DNA half-udg Illumina NovaSeq 6000 PAIRED WGS 1329592756 ERR11435697 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/097/ERR11435697/ERR11435697_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR114/097/ERR11435697/ERR11435697_2.fastq.gz ae96523cb62dbd7cd7c27530039eff97;7617998ef105698c866d6cdedf8710ea 30549343594;29093388600 Parker2023 2023 10.1371/journal.ppat.1011404 KRA004 ENA PRJEB61096 ERS14884856 KRA004.A0101 single AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED Targeted-Capture 10220738 ERR11202909 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR112/009/ERR11202909/ERR11202909_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR112/009/ERR11202909/ERR11202909_2.fastq.gz dfa4f293ebb5a3665e42cfc1fd3b6813;25c71f69827adf0792e04c90e0a39e0e 186251653;192557211 Parker2023 2023 10.1371/journal.ppat.1011404 KRA004 ENA PRJEB61096 ERS14884856 KRA004.A0101 single AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED Targeted-Capture 10278910 ERR11202910 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR112/010/ERR11202910/ERR11202910_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR112/010/ERR11202910/ERR11202910_2.fastq.gz 64a0b23736ea265ae7d43f983e684a01;cfc866608423cfdabd08dff49baca0ee 192588589;185849366 Parker2023 2023 10.1371/journal.ppat.1011404 KRA004 ENA PRJEB61096 ERS14884857 KRA004.A0201 single AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED Targeted-Capture 9525042 ERR11202911 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR112/011/ERR11202911/ERR11202911_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR112/011/ERR11202911/ERR11202911_2.fastq.gz d1bd6bae76cafd5dd3ccdefa6cb6a602;66422058317bd7ecc84d03360253e523 172581354;178547024 From 16ecad69cdae267789283afddecc95c72b556cf5 Mon Sep 17 00:00:00 2001 From: marcel-keller <61977721+marcel-keller@users.noreply.github.com> Date: Mon, 9 Dec 2024 17:08:14 +0100 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cf2f7dfb..77980c98 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,8 @@ and this project follows to [Calendar Versioning](https://calver.org/). ### Changed +- Fixed library typ (half-UDG) for Bonczarowska 2023 10.1098/rspb.2023.0622 (@marcel-keller) + ### Removed ## v24.09: Medieval Town of ToruĊ„ From fa5f8d1b0018c84583a824f6fdd50a9818d060f3 Mon Sep 17 00:00:00 2001 From: marcel-keller <61977721+marcel-keller@users.noreply.github.com> Date: Wed, 11 Dec 2024 13:31:26 +0100 Subject: [PATCH 3/3] Update CHANGELOG.md Co-authored-by: James A. Fellows Yates --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 77980c98..d776b616 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,7 +17,7 @@ and this project follows to [Calendar Versioning](https://calver.org/). ### Changed -- Fixed library typ (half-UDG) for Bonczarowska 2023 10.1098/rspb.2023.0622 (@marcel-keller) +- Bonczarowska2023: Fixed library type (actually half-UDG, despite paper reporting non-UDG) 10.1098/rspb.2023.0622 (fixed by @marcel-keller) ### Removed