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Add package: 2024_Sharko_BIA_Koban #147

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f8141a0
added SSF for 2024_Sharko_BIA_Koban package
Aug 4, 2025
ebca6e7
added SSF for 2023_Guarino-Vignon_MenteshTepe package
Aug 4, 2025
2db9e71
Merge branch 'main' into main
TCLamnidis Aug 6, 2025
9f3e4bf
Merge branch 'poseidon-framework:main' into main
AyGhal Jul 14, 2026
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10 changes: 10 additions & 0 deletions packages/2023_Guarino-Vignon_MenteshTepe/2023_Guarino-Vignon_MenteshTepe.ssf
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poseidon_IDs udg library_built notes run_accession study_accession sample_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp submitted_md5
MT26 minus ds n/a ERR9979363 PRJEB54894 SAMEA110398688 MT26 ERS12496711 2023-01-03 2023-01-03 NextSeq 500 PAIRED GENOMIC ILLUMINA MT26_2020 OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/003/ERR9979363/ERR9979363_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/003/ERR9979363/ERR9979363_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/003/ERR9979363/ERR9979363_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/003/ERR9979363/ERR9979363_2.fastq.gz 1314779780;1339932354 e678ead14d0b94161a9da3131379c143;0d62cd13af6495d586c5de12ff03433d 62421650 ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979363/MT26_R1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979363/MT26_R2.fastq.gz bd3b9d1701b7d1dcaa606f04c55e9b81;f17d24dfcb833d125da700c4e05e76e8
MT23 minus ds n/a ERR9979365 PRJEB54894 SAMEA110398687 MT23 ERS12496710 2023-01-03 2023-01-03 NextSeq 500 PAIRED GENOMIC ILLUMINA MT23_2021 OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/005/ERR9979365/ERR9979365_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/005/ERR9979365/ERR9979365_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/005/ERR9979365/ERR9979365_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/005/ERR9979365/ERR9979365_2.fastq.gz 2562540574;2625145643 e4c421de17059d2a098303e064e7f7ce;0d0639459606961e0602b7232ee2f127 121063278 ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979365/MT23_R1_2021.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979365/MT23_R2_2021.fastq.gz 75d89daa40bf60df0a46e47a462f79c7;64f436b20c723cb8304419d1f40c5f8f
MT23 minus ds n/a ERR9979347 PRJEB54894 SAMEA110398687 MT23 ERS12496710 2023-01-03 2023-01-03 NextSeq 500 SINGLE GENOMIC ILLUMINA NA OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/007/ERR9979347/ERR9979347.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/007/ERR9979347/ERR9979347.fastq.gz 490148522 b06cb633223e897d72e94fdd6716a562 10636555 ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979347/MT23.fastq.combined.fq.prefixed.mapped.mappedonly.sorted.qF.sorted.cleaned.merged_rmdup.clean.RG_sort.rescaled.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979347/MT23.fastq.combined.fq.prefixed.mapped.mappedonly.sorted.qF.sorted.cleaned.merged_rmdup.clean.RG_sort.rescaled.bam.bai 25c1b39a4f6924532ee010615581da82;6aca9bf6effbd48dac97a6efdeb9b3e4
MT26 minus ds n/a ERR9979348 PRJEB54894 SAMEA110398688 MT26 ERS12496711 2023-01-03 2023-01-03 NextSeq 500 SINGLE GENOMIC ILLUMINA NA OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/008/ERR9979348/ERR9979348.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/008/ERR9979348/ERR9979348.fastq.gz 272658720 a011c5af6360bab21d9a4d55b8a2f992 5897528 ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979348/MT26.fastq.combined.fq.prefixed.mapped.mappedonly.sorted.qF.sorted.cleaned.merged_rmdup.clean.RG_sort.rescaled.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979348/MT26.fastq.combined.fq.prefixed.mapped.mappedonly.sorted.qF.sorted.cleaned.merged_rmdup.clean.RG_sort.rescaled.bam.bai 940ffa81b88d5ad849cfb9d6b73f01dc;740acc7e8eade5256a5cc1d7310a5711
MT7 minus ds n/a ERR9979349 PRJEB54894 SAMEA110398689 MT7 ERS12496712 2023-01-03 2023-01-03 NextSeq 500 SINGLE GENOMIC ILLUMINA NA OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/009/ERR9979349/ERR9979349.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/009/ERR9979349/ERR9979349.fastq.gz 155022875 ee58443affa5d0b6217b5c49d035ca52 3384965 ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979349/MT7.fastq.combined.fq.prefixed.mapped.mappedonly.sorted.qF.sorted.cleaned.merged_rmdup.clean.RG_sort.rescaled.bam;ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979349/MT7.fastq.combined.fq.prefixed.mapped.mappedonly.sorted.qF.sorted.cleaned.merged_rmdup.clean.RG_sort.rescaled.bam.bai 01ddf865f0f42dfc5a26775f4047d5b0;b18f9b3254625416064fc683fe2b41ff
MT23 minus ds n/a ERR9979362 PRJEB54894 SAMEA110398687 MT23 ERS12496710 2023-01-03 2023-01-03 NextSeq 500 PAIRED GENOMIC ILLUMINA MT23_2020 OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/002/ERR9979362/ERR9979362_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/002/ERR9979362/ERR9979362_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/002/ERR9979362/ERR9979362_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/002/ERR9979362/ERR9979362_2.fastq.gz 1406373806;1430687044 02767fcc76c83a64f919a4fc5b6940e4;84bf574d8ab8b51265e966244f936c42 70882922 ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979362/MT23_R1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979362/MT23_R2.fastq.gz 21184b7aa6eb90b554b45a1bc1cf0ec4;48dff489ef20157a49f5583c115d0986
MT7 minus ds n/a ERR9979364 PRJEB54894 SAMEA110398689 MT7 ERS12496712 2023-01-03 2023-01-03 NextSeq 500 PAIRED GENOMIC ILLUMINA MT7_2020 OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/004/ERR9979364/ERR9979364_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/004/ERR9979364/ERR9979364_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/004/ERR9979364/ERR9979364_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/004/ERR9979364/ERR9979364_2.fastq.gz 1130350366;1146517367 c6e18f48c6d87ffb13b1548875be1f51;010e4beb0646d93669effa7896b71a38 53783246 ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979364/MT7_R1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979364/MT7_R2.fastq.gz 4f4fac73545b2bfc8abd672ee2550a87;17733d0d014b86da67d6dc2288717531
MT26 minus ds n/a ERR9979366 PRJEB54894 SAMEA110398688 MT26 ERS12496711 2023-01-03 2023-01-03 NextSeq 500 PAIRED GENOMIC ILLUMINA MT26_2021 OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/006/ERR9979366/ERR9979366_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/006/ERR9979366/ERR9979366_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/006/ERR9979366/ERR9979366_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/006/ERR9979366/ERR9979366_2.fastq.gz 2730931605;2769275794 829f7521b4455087c9a182f935eb8bcd;f1b237c9e17310d9f58e9a5e850140a9 121487348 ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979366/MT26_R1_2021.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979366/MT26_R2_2021.fastq.gz b942f4388e0be86dec772fec2eae4816;cf5ee173e4d75c053ff8c8c1504decd6
MT7 minus ds n/a ERR9979367 PRJEB54894 SAMEA110398689 MT7 ERS12496712 2023-01-03 2023-01-03 NextSeq 500 PAIRED GENOMIC ILLUMINA MT7_2021 OTHER ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/007/ERR9979367/ERR9979367_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR997/007/ERR9979367/ERR9979367_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/007/ERR9979367/ERR9979367_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/ERR997/007/ERR9979367/ERR9979367_2.fastq.gz 3925849296;3967910568 68b806640ad6264281e6ef5aeed997cb;28304cb2018d30ba9948c52494734f47 175855200 ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979367/MT7_R1_2021.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR997/ERR9979367/MT7_R2_2021.fastq.gz 996d918dbeb1b0eab056ffe98832e0f5;9abfe5628237966af5231b2249165bbd
7 changes: 7 additions & 0 deletions packages/2024_Sharko_BIA_Koban/2024_Sharko_BIA_Koban.ssf
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poseidon_IDs udg library_built notes run_accession study_accession sample_accession sample_alias secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_ftp fastq_aspera fastq_bytes fastq_md5 read_count submitted_ftp submitted_md5
al40 half ds n/a SRR17660970 PRJNA797283 SAMN25084273 Bratskoe 1st barrow cemetery 1402 SRS11707708 2022-01-21 2022-01-21 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA Lib40al WGA ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/070/SRR17660970/SRR17660970_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/070/SRR17660970/SRR17660970_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/070/SRR17660970/SRR17660970_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/070/SRR17660970/SRR17660970_2.fastq.gz 3611506120;3665958378 a304fd79285cf9cf1c20c0afd20a294d;fed3d5a03f8c9cb5c077ec9e7837ca88 61739921
al7 half ds n/a SRR17660974 PRJNA797283 SAMN25084269 Zayukovo-3 72 SRS11707704 2022-01-20 2022-01-20 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA Lib7al WGA ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/074/SRR17660974/SRR17660974_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/074/SRR17660974/SRR17660974_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/074/SRR17660974/SRR17660974_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/074/SRR17660974/SRR17660974_2.fastq.gz 6748900594;6989039871 717e8f05662dacc25bf88975b0099f4d;c7114885ceb887fb41a76850b71bb27b 102310464
al2 half ds n/a SRR17660975 PRJNA797283 SAMN25084268 Klin-Yar III 355 SRS11707703 2022-01-21 2022-01-21 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA Lib2Nal WGA ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/075/SRR17660975/SRR17660975_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/075/SRR17660975/SRR17660975_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/075/SRR17660975/SRR17660975_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/075/SRR17660975/SRR17660975_2.fastq.gz 7694906780;7942436727 01ba5f6d70b3e62e30f285fd25400c21;c61719a8b714941f6edf902d9cc78b0f 122179212
al11 half ds n/a SRR17660971 PRJNA797283 SAMN25084272 Zayukovo-3 82 SRS11707707 2022-01-21 2022-01-21 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA Lib11al WGA ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/071/SRR17660971/SRR17660971_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/071/SRR17660971/SRR17660971_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/071/SRR17660971/SRR17660971_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/071/SRR17660971/SRR17660971_2.fastq.gz 9161994400;9506144052 032fbb2f13da9dcf2f38cf1fc600531d;426f19bd0f4354b7300974774a963283 140898436
al8 half ds n/a SRR17660973 PRJNA797283 SAMN25084270 Zayukovo-3 79 SRS11707705 2022-01-22 2022-01-22 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA Lib8al WGA ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/073/SRR17660973/SRR17660973_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/073/SRR17660973/SRR17660973_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/073/SRR17660973/SRR17660973_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/073/SRR17660973/SRR17660973_2.fastq.gz 14712286322;15095784144 81ec4a6570f581429694805d5beb4633;4235914785b9d5f343682d085eaa7602 226532095
al9 half ds n/a SRR17660972 PRJNA797283 SAMN25084271 Zayukovo-3 80 SRS11707706 2022-01-22 2022-02-05 Illumina NovaSeq 6000 PAIRED GENOMIC ILLUMINA Lib9al WGA ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/072/SRR17660972/SRR17660972_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR176/072/SRR17660972/SRR17660972_2.fastq.gz fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/072/SRR17660972/SRR17660972_1.fastq.gz;fasp.sra.ebi.ac.uk:/vol1/fastq/SRR176/072/SRR17660972/SRR17660972_2.fastq.gz 10694090125;10900345717 486c4ae9838e1b3107331288db324920;5d3d60043fa5f6dbef9799bd94f0c1b8 159729007
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