diff --git a/2021_CarlhoffNature/2021_CarlhoffNature.bed b/2021_CarlhoffNature/2021_CarlhoffNature.bed new file mode 100644 index 0000000..9e99fac --- /dev/null +++ b/2021_CarlhoffNature/2021_CarlhoffNature.bed @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e9c683ca3252b406baea29a4b09d787bf584a73bdb5d4f81c587334de8e93d9d +size 1233016 diff --git a/2021_CarlhoffNature/2021_CarlhoffNature.bib b/2021_CarlhoffNature/2021_CarlhoffNature.bib new file mode 100644 index 0000000..8fbcf0b --- /dev/null +++ b/2021_CarlhoffNature/2021_CarlhoffNature.bib @@ -0,0 +1,16 @@ +@ARTICLE{CarlhoffNature2021, +title = "{Genome of a middle Holocene hunter-gatherer from Wallacea}", +author = "Carlhoff, Selina and Duli, Akin and N{\"a}gele, Kathrin and Nur, Muhammad and Skov, Laurits and Sumantri, Iwan and Oktaviana, Adhi Agus and Hakim, Budianto and Burhan, Basran and Syahdar, Fardi Ali and McGahan, David P and Bulbeck, David and Perston, Yinika L and Newman, Kim and Saiful, Andi Muhammad and Ririmasse, Marlon and Chia, Stephen and {Hasanuddin} and Pulubuhu, Dwia Aries Tina and {Suryatman} and {Supriadi} and Jeong, Choongwon and Peter, Benjamin M and Pr{\"u}fer, Kay and Powell, Adam and Krause, Johannes and Posth, Cosimo and Brumm, Adam", +journal = "Nature", +volume = 596, +number = 7873, +pages = "543--547", +month = aug, +year = 2021, +url = "http://dx.doi.org/10.1038/s41586-021-03823-6", +language = "en", +issn = "0028-0836, 1476-4687", +pmid = "34433944", +doi = "10.1038/s41586-021-03823-6", +pmc = "PMC8387238" +} diff --git a/2021_CarlhoffNature/2021_CarlhoffNature.bim b/2021_CarlhoffNature/2021_CarlhoffNature.bim new file mode 100644 index 0000000..384f3bc --- /dev/null +++ b/2021_CarlhoffNature/2021_CarlhoffNature.bim @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f3d3c4aaa95fc68acd08d9695f14fc8e777d6078d59a2ca64bdaeb770d135d4e +size 43313767 diff --git a/2021_CarlhoffNature/2021_CarlhoffNature.fam b/2021_CarlhoffNature/2021_CarlhoffNature.fam new file mode 100644 index 0000000..1ea6111 --- /dev/null +++ b/2021_CarlhoffNature/2021_CarlhoffNature.fam @@ -0,0 +1,2 @@ +Leang_Panninge GUP001_MNT 0 0 2 0 +Leang_Panninge GUP001_ss_MNT 0 0 2 0 diff --git a/2021_CarlhoffNature/2021_CarlhoffNature.janno b/2021_CarlhoffNature/2021_CarlhoffNature.janno new file mode 100644 index 0000000..901b54d --- /dev/null +++ b/2021_CarlhoffNature/2021_CarlhoffNature.janno @@ -0,0 +1,3 @@ +Poseidon_ID Genetic_Sex Group_Name Alternative_IDs Relation_To Relation_Degree Relation_Type Relation_Note Collection_ID Country Country_ISO Location Site Latitude Longitude Date_Type Date_C14_Labnr Date_C14_Uncal_BP Date_C14_Uncal_BP_Err Date_BC_AD_Start Date_BC_AD_Median Date_BC_AD_Stop Date_Note MT_Haplogroup Y_Haplogroup Source_Tissue Nr_Libraries Library_Names Capture_Type UDG Library_Built Genotype_Ploidy Data_Preparation_Pipeline_URL Endogenous Nr_SNPs Coverage_on_Target_SNPs Damage Contamination Contamination_Err Contamination_Meas Contamination_Note Genetic_Source_Accession_IDs Primary_Contact Publication Note Keywords Eager_ID Individual_ID RateErrX RateErrY RateX RateY +GUP001_MNT F Leang_Panninge n/a GUP001_ss_MNT identical same_as n/a 30 B. PANNINGE Skull block region 9 petrous Indonesia ID Southern Sulawesi Leang Panninge -4.7741 119.9396 C14 Wk-48639 6317 19 -5314 -5265 -5215 n/a M n/a bone_petrous 1 GUP001.A0101 1240K;Shotgun half ds haploid https://github.com/nf-core/eager/releases/tag/2.4.6 6.762222 272731 n/a 0.4636218846261551 0.11128 3.536035e-14 ANGSD[v0.935] Nr Snps (per library): 691. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB43715;ERS5956814;ERR5490520;ERR5490521;ERR5490522;ERR5490523;ERR5490524;ERR5490525;ERR5490526 Selina Carlhoff CarlhoffNature2021 C14 dates from charcoal and seeds associated with burial; damage for ds SG; mtcontam for ss with AuthentiCT n/a GUP001 GUP001 0.007582631999185001 0.001447150678242 0.8115348979428191 0.020098725775262002 +GUP001_ss_MNT F Leang_Panninge n/a GUP001_MNT identical same_as n/a 30 B. PANNINGE Skull block region 9 petrous Indonesia ID Southern Sulawesi Leang Panninge -4.7741 119.9396 C14 Wk-48639 6317 19 -5314 -5265 -5215 n/a M n/a bone_petrous 1 GUP001.A0102 1240K;Shotgun minus ss haploid https://github.com/nf-core/eager/releases/tag/2.4.6 13.339985 134067 n/a 0.5877457008717157 0.097276 3.860919e-15 ANGSD[v0.935] Nr Snps (per library): 345. Estimate and error are weighted means of values per library. Libraries with fewer than 100 SNPs used in contamination estimation were excluded. PRJEB43715;ERS5956814;ERR5490527;ERR5490528;ERR5490529 Selina Carlhoff CarlhoffNature2021 C14 dates from charcoal and seeds associated with burial; damage for ds SG; mtcontam for ss with AuthentiCT n/a GUP001_ss GUP001 0.008514648295196001 0.0016382538785210002 0.7711635308594431 0.019378750752398 diff --git a/2021_CarlhoffNature/2021_CarlhoffNature.ssf b/2021_CarlhoffNature/2021_CarlhoffNature.ssf new file mode 100644 index 0000000..5ea72cc --- /dev/null +++ b/2021_CarlhoffNature/2021_CarlhoffNature.ssf @@ -0,0 +1,11 @@ +sample_accession study_accession run_accession sample_alias poseidon_IDs udg library_built secondary_sample_accession first_public last_updated instrument_model library_layout library_source instrument_platform library_name library_strategy fastq_aspera fastq_bytes fastq_md5 fastq_ftp read_count submitted_ftp +SAMEA8270508 PRJEB43715 ERR5490520 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/000/ERR5490520/ERR5490520.fastq.gz 31485654 842ec55a3a0aff4979dea1b5dc529e7c ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/000/ERR5490520/ERR5490520.fastq.gz 945210 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490520/GUP001.A0101.MT1.1.fastq.truncated.gz +SAMEA8270508 PRJEB43715 ERR5490521 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/001/ERR5490521/ERR5490521.fastq.gz 32643939 e4c9ae3aed81094a383c2c2003dd961f ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/001/ERR5490521/ERR5490521.fastq.gz 1040533 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490521/GUP001.A0101.MT1.2.fastq.truncated.gz +SAMEA8270508 PRJEB43715 ERR5490522 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/002/ERR5490522/ERR5490522.fastq.gz 192243801 a4add9bc886418c913420eab0391297e ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/002/ERR5490522/ERR5490522.fastq.gz 6189559 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490522/GUP001.A0101.MT1.3.fastq.truncated.gz +SAMEA8270508 PRJEB43715 ERR5490523 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 WGS fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/003/ERR5490523/ERR5490523.fastq.gz 95526960 29a36d22db98919f96d32af631a9422c ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/003/ERR5490523/ERR5490523.fastq.gz 2888875 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490523/GUP001.A0101.SG1.1.fastq.truncated.gz +SAMEA8270508 PRJEB43715 ERR5490524 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/004/ERR5490524/ERR5490524.fastq.gz 562634908 ee58126a3880e12ac25ff3c1adf97aec ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/004/ERR5490524/ERR5490524.fastq.gz 17847250 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490524/GUP001.A0101.TF1.1.fastq.truncated.gz +SAMEA8270508 PRJEB43715 ERR5490525 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/005/ERR5490525/ERR5490525.fastq.gz 1541567827 640a45bc4956b647f5578a66763813d0 ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/005/ERR5490525/ERR5490525.fastq.gz 50108944 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490525/GUP001.A0101.TF1.2.fastq.truncated.gz +SAMEA8270508 PRJEB43715 ERR5490526 GUP001 GUP001_MNT half ds ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0101 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/006/ERR5490526/ERR5490526.fastq.gz 674880719 e58345ddc808d879d255f8d68065050d ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/006/ERR5490526/ERR5490526.fastq.gz 23288459 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490526/GUP001.A0101.TF1.3.fastq.truncated.gz +SAMEA8270508 PRJEB43715 ERR5490527 GUP001 GUP001_ss_MNT minus ss ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0102 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/007/ERR5490527/ERR5490527.fastq.gz 656969967 d16a8f18feef912878f0b56218581717 ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/007/ERR5490527/ERR5490527.fastq.gz 21959304 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490527/GUP001.A0102.AA1.1.fastq.truncated.gz +SAMEA8270508 PRJEB43715 ERR5490528 GUP001 GUP001_ss_MNT minus ss ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0102 WGS fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/008/ERR5490528/ERR5490528.fastq.gz 145599926 e2be513bf56c01591ecdb7dfbe55c5cb ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/008/ERR5490528/ERR5490528.fastq.gz 5086983 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490528/GUP001.A0102.SG1.1.fastq.truncated.gz +SAMEA8270508 PRJEB43715 ERR5490529 GUP001 GUP001_ss_MNT minus ss ERS5956814 2021-06-18 2021-06-18 Illumina HiSeq 4000 SINGLE METAGENOMIC ILLUMINA GUP001.A0102 Targeted-Capture fasp.sra.ebi.ac.uk:/vol1/fastq/ERR549/009/ERR5490529/ERR5490529.fastq.gz 674885210 189d55160fdfec278ddc8fba5296ad18 ftp.sra.ebi.ac.uk/vol1/fastq/ERR549/009/ERR5490529/ERR5490529.fastq.gz 23288459 ftp.sra.ebi.ac.uk/vol1/run/ERR549/ERR5490529/GUP001.A0102.TF1.1.fastq.truncated.gz diff --git a/2021_CarlhoffNature/CHANGELOG.md b/2021_CarlhoffNature/CHANGELOG.md new file mode 100644 index 0000000..753a055 --- /dev/null +++ b/2021_CarlhoffNature/CHANGELOG.md @@ -0,0 +1,8 @@ +- V 1.0.0: Bump version for release +- V 0.1.7: Update .bib +- V 0.1.6: Add contributor and description +- V 0.1.5: Remove abstract from .bib file +- V 0.1.4: Add Country_ISO info +- V 0.1.3: Fill-in metadata from community-archive: 2021_CarlhoffNature-2.2.0 +- V 0.1.2: Add bibtex. Update Genetic_Sex. Add identical individual to Relation_* columns. +- V 0.1.1: Automatic update of janno file from Minotaur processing. diff --git a/2021_CarlhoffNature/POSEIDON.yml b/2021_CarlhoffNature/POSEIDON.yml new file mode 100644 index 0000000..b019843 --- /dev/null +++ b/2021_CarlhoffNature/POSEIDON.yml @@ -0,0 +1,26 @@ +poseidonVersion: 2.7.1 +title: 2021_CarlhoffNature +description: Genome of a Middle Holocene hunter-gatherer from Wallacea +contributor: +- name: Thiseas C. Lamnidis + email: thiseas_christos_lamnidis@eva.mpg.de + orcid: 0000-0003-4485-8570 +packageVersion: 1.0.0 +lastModified: 2024-04-08 +genotypeData: + format: PLINK + genoFile: 2021_CarlhoffNature.bed + genoFileChkSum: 079d15ad25a6db3f7e3d1da9e105abc3 + snpFile: 2021_CarlhoffNature.bim + snpFileChkSum: 433fa85a23f3123bade02348e4628b75 + indFile: 2021_CarlhoffNature.fam + indFileChkSum: d5982f4cd410501dd26c0b2f2b95a83b + snpSet: 1240K +jannoFile: 2021_CarlhoffNature.janno +jannoFileChkSum: 9b1fc8f11211767fbb5868128327a6cd +sequencingSourceFile: 2021_CarlhoffNature.ssf +sequencingSourceFileChkSum: ac4cec11100b5ab343548313c86c68b2 +bibFile: 2021_CarlhoffNature.bib +bibFileChkSum: 64bcfc5f95b953b526b559f09a43c72c +readmeFile: README.md +changelogFile: CHANGELOG.md diff --git a/2021_CarlhoffNature/README.md b/2021_CarlhoffNature/README.md new file mode 100644 index 0000000..b7bb345 --- /dev/null +++ b/2021_CarlhoffNature/README.md @@ -0,0 +1,53 @@ +# 2021_CarlhoffNature + +This package was created on 2024-04-03 and was processed using the following versions: + +- nf-core/eager version: 2.4.6 +- Minotaur config version: 0.2.1dev +- CaptureType profile: 1240K +- CaptureType config version: 0.2.2dev +- Config template version: 0.3.0dev +- Package config version: 0.3.0dev +- Minotaur-packager version: 0.3.0dev +- populate_janno.py version: 0.3.2dev + +## Fill relevant columns from the community archive package. + +```bash +## First fill-in missing metadata from relevant columns (no processing-based info). +trident jannocoalesce \ + -s ../../archives/community-archive/2021_CarlhoffNature-2.2.0/2021_CarlhoffNature.janno \ + -t 2021_CarlhoffNature/2021_CarlhoffNature.janno \ + --stripIdRegex "(_ss_MNT$)|(_MNT$)" \ + --includeColumns Alternative_IDs,Relation_To,Relation_Degree,Relation_Type,Relation_Note,Collection_ID,Country,Country_ISO,Location,Site,Latitude,Longitude,Date_Type,Date_C14_Labnr,Date_C14_Uncal_BP,Date_C14_Uncal_BP_Err,Date_BC_AD_Start,Date_BC_AD_Median,Date_BC_AD_Stop,Date_Note,MT_Haplogroup,Y_Haplogroup,Source_Tissue,Primary_Contact,Note,Keywords + +## Then fill in Group_Name and Genetic_Sex +trident jannocoalesce \ + -s ../../archives/community-archive/2021_CarlhoffNature-2.2.0/2021_CarlhoffNature.janno \ + -t 2021_CarlhoffNature/2021_CarlhoffNature.janno \ + --stripIdRegex "(_ss_MNT$)|(_MNT$)" \ + --includeColumns Genetic_Sex,Group_Name \ + --force + +## Mirror Sex and Group name info to the fam file. +paste -d "\t" 2021_CarlhoffNature/2021_CarlhoffNature.fam <(cut -f 1-3 2021_CarlhoffNature/2021_CarlhoffNature.janno |tail -n +2) | \ + awk ' + BEGIN{ + OFS=IFS="\t" + } + { + $1=$9 + if ($8 == "M") { + $5=1 + } else if ($8 == "F") { + $5=2 + } + print $1,$2,$3,$4,$5,$6 + } + ' > tmp.fam + ## Cannot overwrite in the same command that reads in the file, so an extra mv is needed. + mv tmp.fam 2021_CarlhoffNature/2021_CarlhoffNature.fam + + ## trident version: 1.4.1.0 + trident rectify --packageVersion Patch --logText "Fill-in metadata from community-archive: 2021_CarlhoffNature-2.2.0" --checksumAll -d . +```