cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.3535/hv7-7xl-8xf
title: Inga ciliata subsp. ciliata

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/yml-5zy-ytl
title: Nidorella undulata (Thunb.) Sond. ex Harv.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/31p-4r8-008
title: Persicaria meisneriana (Cham. & Schltdl.) M. Gómez

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/lel-1yg-faq
title: Trichilia catigua A. Juss.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/hlb-h9c-z7s
title: Lippia acutidens Mart. & Schauer

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/6lt-3q3-5nd
title: Potamogeton amplifolius Tuck.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/bw3-x9j-yyg
title: Inga laurina (Sw.) Willd.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/6aj-65b-91h
title: Symplocos Jacq.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/z43-ge4-eke
title: Verbascum bithynicum Boiss.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/ch7-hav-034
title: Echinophora sibthorpiana Guss.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/vfc-68n-gy2
title: Osmitopsis nana Schltr.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.15468/dl.7prd8w
title: Occurrence Download

description: A dataset containing 160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "MediaType is Image",
 "TaxonKey is Neoraputia alba"
 ]
}

 The dataset includes 160 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0063167-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/ct4-26m-0fc
title: Lippia sericea Cham.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/b2p-ylc-awb
title: Trigonia spruceana Benth. ex Warm.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/lv5-gn2-mlj
title: Silene sendtneri subsp. balcanica (Formánek) Greuter

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/saq-jp2-a46
title: Eremopyrum orientale (L.) Jaub. & Spach

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/2az-lea-qg0
title: Agropyron cristatum (L.) Gaertn.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/9yg-dc8-dsc
title: Cleidion amazonicum Ule

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/br8-b4p-64z
title: Inga cayennensis Sagot ex Benth.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/9l9-mmz-6k7
title: Aloysia chamaedryfolia Cham.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/bjg-01r-sva
title: Lacistema polystachyum Schnizl.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/87e-1qy-rea
title: Trinia scabra Boiss. & Noë

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/pnb-77w-zzy
title: Melasma melampyroides (Rich.) Pennell ex Britton & Wilson

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/a35-cdp-x69
title: Orbivestus leopoldii (Sch. Bip. ex Walp.) H. Rob.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/pq5-p4d-hca
title: Alyssum armenum Boiss.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/m8h-y61-ef8
title: Inga umbellifera (Vahl) Steud. ex DC.

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.3535/rnt-4w9-n70
title: Pilea fendleri Killip

description: Digital Specimen for the physical specimen hosted at University of Graz.
DOI: 10.15468/dl.vqm4ec
title: Occurrence Download

description: A dataset containing 2193 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Philothamnus semivariegatus (Smith, 1840)"
 ]
}

 The dataset includes 2193 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092431-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/pkbq6l
title: 2244.wav

description: :unav
DOI: 10.15468/dl.nw2w39
title: Occurrence Download

description: A dataset containing 8973 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dioscorea bulbifera L.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 8973 records from 279 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092429-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/wbkfre
title: 2163.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/8siejd
title: 2243.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/uofygt
title: 2544.wav

description: :unav
DOI: 10.60600/yu/clawet/sc88f1
title: 2204.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/0ywrqn
title: 2510.wav

description: :unav
DOI: 10.60600/yu/clawet/gdowkn
title: 2329.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/t5eg8a
title: 2218.wav

description: :unav
DOI: 10.60600/yu/clawet/mc894n
title: 2490.wav

description: :unav
DOI: 10.60600/yu/clawet/2tkixc
title: 2121.wav

description: :unav
DOI: 10.60600/yu/clawet/it0y1r
title: 2227.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/l9pprv
title: 2532.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/toonde
title: 2159.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/mup120
title: 2158.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/s8o3hm
title: 2311.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/8gc1zk
title: 2143.wav

description: :unav
DOI: 10.60600/yu/clawet/vvyxzh
title: 2481.wav

description: :unav
DOI: 10.60600/yu/clawet/em9aab
title: 2279.wav

description: :unav
DOI: 10.60600/yu/clawet/igxgpc
title: 2480.TextGrid

description: :unav
DOI: 10.15468/dl.84ag6y
title: Occurrence Download

description: A dataset containing 197 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dioscorea nummularia Lam.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 197 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092434-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/taewga
title: 2181.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/enyfna
title: 2258.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/sqwoqj
title: 2568.wav

description: :unav
DOI: 10.60600/yu/clawet/u4o5wx
title: 2355.wav

description: :unav
DOI: 10.60600/yu/clawet/ofv656
title: 2124.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/yqs6ad
title: 2473.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/kpwjwa
title: 2327.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/8nqut1
title: 2503.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/mfq4fx
title: 2429.wav

description: :unav
DOI: 10.60600/yu/clawet/c1rp3p
title: 2495.wav

description: :unav
DOI: 10.60600/yu/clawet/4t5itc
title: 2130.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/pl6pmn
title: 2376.wav

description: :unav
DOI: 10.60600/yu/clawet/hlfhaw
title: 2234.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/dhskqd
title: 2226.wav

description: :unav
DOI: 10.15468/dl.r4kyzh
title: Occurrence Download

description: A dataset containing 69324 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Ireland, Svalbard and Jan Mayen, Portugal, Spain, France, Germany, Belgium, Netherlands, Denmark, Estonia, Latvia, Lithuania, Italy, Greece, Cyprus, Türkiye, Russian Federation, Ukraine, Romania, Bulgaria, Albania, Croatia, Austria, Slovakia, Poland)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Senecio sylvaticus L."
 ]
}

 The dataset includes 69324 records from 631 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092430-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/rujsmo
title: 2570.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/qfb0kj
title: 2523.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/leorys
title: 2318.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/a69zbz
title: 2310.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/cypcpk
title: 2271.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/em4kop
title: 2276.wav

description: :unav
DOI: 10.60600/yu/clawet/xdsgjf
title: 2404.wav

description: :unav
DOI: 10.17028/rd.lboro.25722384
title: DATASETS HEATSHIELD project Loughborough University, averaged per condition and individual sessions, and files showing the statistical analyses.

description: The purpose of this study was to investigate which climate/heat indices perform best in predicting heat-induced loss of physical work capacity (PWC-loss). Integrating data from earlier studies, data from 982 exposures (75 conditions) exercising at a fixed cardiovascular load of 130b.min<sup>-1</sup>, in varying temperatures (15-50°C), humidities (20-80%), solar radiation (0-800W.m<sup>-2</sup>), wind (0.2-3.5m.s<sup>-1</sup>) and two clothing levels, were used to model the predictive power of ambient temperature, Universal Thermal Climate Index (UTCI), Wet Bulb Globe Temperature (WBGT), Modified Equivalent Temperature (mPET), Heat Index, Apparent Temperature (AT), and Wet Bulb Temperature (<i>T</i><sub><em>wb</em></sub>) for the calculation of PWC-loss, skin temperature (<i>T</i><sub>skin</sub>) and core-to-skin temperature gradient, and Thermal perception( TSV) in the heat. R<sup>2</sup>, RMSD and Akaike stats were used indicating model performance.Indices not including wind/radiation in their calculation (<i>T</i><sub><em>a</em></sub>, Heat Index, AT, <i>T</i><sub><em>wb</em></sub>) struggled to provide consistent predictions across variables. For PWC-loss and TSV, UTCI and WBGT had the highest predictive power. For <i>T</i><sub>skin</sub>, and core-to-skin temperature gradient, the physiological models UTCI and mPET worked best in semi-nude conditions, but clothed, AT, WBGT and UTCI worked best. For all index predictions, <i>T</i><sub><em>a</em></sub>, vapor pressure and <i>T</i><sub>wb</sub> were shown to be the worst heat strain predictors. While UTCI and WBGT had similar model performance using the full dataset, WBGT did not work appropriately in windy, hot-dry, conditions where WBGT predicted lower strain due to wind, whereas the empirical data, UTCI and mPET indicated that wind in fact increased the overall level of thermal strain. The findings of the current study highlight the advantages of using a physiological model-based index like UTCI when evaluating heat stress in dynamic thermal environments.
DOI: 10.60600/yu/clawet/ebinf8
title: 2180.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/cyiuvs
title: 2099.wav

description: :unav
DOI: 10.15468/dl.wsebn5
title: Occurrence Download

description: A dataset containing 375 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dioscorea sansibarensis Pax)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 375 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092435-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/wydbka
title: 2340.wav

description: :unav
DOI: 10.60600/yu/clawet/cknpxv
title: 2301.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/l5ah1c
title: 2230.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/77ptgx
title: 2507.TextGrid

description: :unav
DOI: 10.17028/rd.lboro.25722384.v2
title: DATASETS HEATSHIELD project Loughborough University, averaged per condition and individual sessions, and files showing the statistical analyses.

description: The purpose of this study was to investigate which climate/heat indices perform best in predicting heat-induced loss of physical work capacity (PWC-loss). Integrating data from earlier studies, data from 982 exposures (75 conditions) exercising at a fixed cardiovascular load of 130b.min<sup>-1</sup>, in varying temperatures (15-50°C), humidities (20-80%), solar radiation (0-800W.m<sup>-2</sup>), wind (0.2-3.5m.s<sup>-1</sup>) and two clothing levels, were used to model the predictive power of ambient temperature, Universal Thermal Climate Index (UTCI), Wet Bulb Globe Temperature (WBGT), Modified Equivalent Temperature (mPET), Heat Index, Apparent Temperature (AT), and Wet Bulb Temperature (<i>T</i><sub><em>wb</em></sub>) for the calculation of PWC-loss, skin temperature (<i>T</i><sub>skin</sub>) and core-to-skin temperature gradient, and Thermal perception( TSV) in the heat. R<sup>2</sup>, RMSD and Akaike stats were used indicating model performance.Indices not including wind/radiation in their calculation (<i>T</i><sub><em>a</em></sub>, Heat Index, AT, <i>T</i><sub><em>wb</em></sub>) struggled to provide consistent predictions across variables. For PWC-loss and TSV, UTCI and WBGT had the highest predictive power. For <i>T</i><sub>skin</sub>, and core-to-skin temperature gradient, the physiological models UTCI and mPET worked best in semi-nude conditions, but clothed, AT, WBGT and UTCI worked best. For all index predictions, <i>T</i><sub><em>a</em></sub>, vapor pressure and <i>T</i><sub>wb</sub> were shown to be the worst heat strain predictors. While UTCI and WBGT had similar model performance using the full dataset, WBGT did not work appropriately in windy, hot-dry, conditions where WBGT predicted lower strain due to wind, whereas the empirical data, UTCI and mPET indicated that wind in fact increased the overall level of thermal strain. The findings of the current study highlight the advantages of using a physiological model-based index like UTCI when evaluating heat stress in dynamic thermal environments.
DOI: 10.60600/yu/clawet/icqae2
title: 2083.wav

description: :unav
DOI: 10.60600/yu/clawet/5dnvv1
title: 2292.wav

description: :unav
DOI: 10.60600/yu/clawet/sayiwc
title: 2304.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/cekell
title: 2409.wav

description: :unav
DOI: 10.60600/yu/clawet/6t7ovn
title: 2409.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/hglh99
title: 2578.wav

description: :unav
DOI: 10.60600/yu/clawet/9gwxjb
title: 2422.wav

description: :unav
DOI: 10.60600/yu/clawet/lmzp01
title: 2461.TextGrid

description: :unav
DOI: 10.15468/dl.h5yk3j
title: Occurrence Download

description: A dataset containing 534 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhododendron ambiguum Hemsl."
 ]
}

 The dataset includes 534 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092436-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/lo1smq
title: 2301.wav

description: :unav
DOI: 10.60600/yu/clawet/pkhaib
title: 2447.wav

description: :unav
DOI: 10.60600/yu/clawet/f8clqu
title: 2326.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/pqw0ih
title: 2339.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/gb1dao
title: 2571.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/wlwukw
title: 2477.TextGrid

description: :unav
DOI: 10.15468/dl.dkhuq8
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dioscorea glomerulata Hauman)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 58 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0092437-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60600/yu/clawet/lqvdl9
title: 2287.wav

description: :unav
DOI: 10.60600/yu/clawet/g1qayv
title: 2455.wav

description: :unav
DOI: 10.60600/yu/clawet/l9zvft
title: 2380.wav

description: :unav
DOI: 10.60600/yu/clawet/3qszxg
title: 2426.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/lhnb5r
title: 2560.wav

description: :unav
DOI: 10.60600/yu/clawet/mkwhrs
title: 2110.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/10jfwb
title: 2552.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/rfu63j
title: 2414.wav

description: :unav
DOI: 10.18712/nsd-nsd3176-v1
title: Attitudes towards paternalistic interventions to prevent the spread of COVID-19

description: The purpose of this study is to examine differences in attitudes towards hard and soft state interventions to prevent the spread of COVID-19. The project investigates how individuals perceive that soft and hard interventions will work to prevent the spread of COVID-19 in society.
DOI: 10.60600/yu/clawet/sidfap
title: 2432.wav

description: :unav
DOI: 10.6084/m9.figshare.25874389
title: <b>Expanding the Lens: Integrating Social Sciences and Humanities into the Computational Reproducibility Dialogue</b>

description: The purpose of this critical analysis of Varga's (2024) article "Researchers' contribution needed! - New survey on computational reproducibility is open" is to get an understanding of the relationship between the creation of multidisciplinary knowledge and its application to the social and humanities disciplines. The emphasis is on pertinent evaluations for various fields in keeping with Varga's (2024b) premise.
DOI: 10.6084/m9.figshare.25874389.v1
title: <b>Expanding the Lens: Integrating Social Sciences and Humanities into the Computational Reproducibility Dialogue</b>

description: The purpose of this critical analysis of Varga's (2024) article "Researchers' contribution needed! - New survey on computational reproducibility is open" is to get an understanding of the relationship between the creation of multidisciplinary knowledge and its application to the social and humanities disciplines. The emphasis is on pertinent evaluations for various fields in keeping with Varga's (2024b) premise.
DOI: 10.60600/yu/clawet/2fuc74
title: 2210.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/jpifsy
title: 2499.TextGrid

description: :unav
DOI: 10.60600/yu/clawet/4k90zv
title: 2359.wav

description: :unav
DOI: 10.60600/yu/clawet/synglk
title: 2566.wav

description: :unav
DOI: 10.60600/yu/clawet/5yqirc
title: 2516.wav

description: :unav
DOI: 10.5281/zenodo.12166291
title: Bin-assembled Escherichia coli genomes from a study in Punjab, Pakistan

description: Bin-assembled Escherichia coli genomes from Punjab, Pakistan

These assemblies are a part of a cross-sectional study conducted in Punjab, Pakistan aimed at investigating E. coli colonisation diversity in healthy carriage with the use of CLED enrichment plates.

About

Version history

v0.1.1 (current version)



Added reference to the study.


v0.1.0



Added brief description with a few missing parts.


Distribution

If you use these assemblies in your study please cite the source as appropriate. These assemblies are made available under a CC-BY 4.0 license.

Citation

Khawaja, T., Mäklin, T., Kallonen, T. et al. Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nature Communications 15, 5196 (2024). https://doi.org/10.1038/s41467-024-49591-5

Methods briefly

Species identification

Sequencing data from the ENA project PRJEB36642 was error-corrected with fastp and pseudoaligned with Themisto against a species-level index (available from https://doi.org/10.5281/zenodo.6656881). Reads were assigned to species using the mSWEEP/mGEMS pipeline as described in https://www.nature.com/articles/s41467-022-35178-5.

Lineage identification

Read from the species-level bins were again pseudoaligned with Themisto against an E. coli index (will be made available in a later version). Lineage-level assignment was performed using mSWEEP and mGEMS at the level of PopPUNK sequence clusters. The created bins were screened with demix_check and bins that received a score of 1 or 2 were kept. Data in the kept bins were assembled with shovill and the bin-assembled genomes (BAGs) were quality controlled with checkm for >= 90% completeness and <= 10% contamination. Finally, BAGs shorter than 4 Mb or longer than 6 Mb were removed.

Contact

Tommi Mäklin <tommi'at'maklin.fi>.
DOI: 10.60600/yu/clawet/sbnrsk
title: 2407.TextGrid

description: :unav
DOI: 10.5281/zenodo.10075670
title: Bin-assembled Escherichia coli genomes from a study in Punjab, Pakistan

description: Bin-assembled Escherichia coli genomes from Punjab, Pakistan

These assemblies are a part of a cross-sectional study conducted in Punjab, Pakistan aimed at investigating E. coli colonisation diversity in healthy carriage with the use of CLED enrichment plates.

About

Version history

v0.1.1 (current version)



Added reference to the study.


v0.1.0



Added brief description with a few missing parts.


Distribution

If you use these assemblies in your study please cite the source as appropriate. These assemblies are made available under a CC-BY 4.0 license.

Citation

Khawaja, T., Mäklin, T., Kallonen, T. et al. Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nature Communications 15, 5196 (2024). https://doi.org/10.1038/s41467-024-49591-5

Methods briefly

Species identification

Sequencing data from the ENA project PRJEB36642 was error-corrected with fastp and pseudoaligned with Themisto against a species-level index (available from https://doi.org/10.5281/zenodo.6656881). Reads were assigned to species using the mSWEEP/mGEMS pipeline as described in https://www.nature.com/articles/s41467-022-35178-5.

Lineage identification

Read from the species-level bins were again pseudoaligned with Themisto against an E. coli index (will be made available in a later version). Lineage-level assignment was performed using mSWEEP and mGEMS at the level of PopPUNK sequence clusters. The created bins were screened with demix_check and bins that received a score of 1 or 2 were kept. Data in the kept bins were assembled with shovill and the bin-assembled genomes (BAGs) were quality controlled with checkm for >= 90% completeness and <= 10% contamination. Finally, BAGs shorter than 4 Mb or longer than 6 Mb were removed.

Contact

Tommi Mäklin <tommi'at'maklin.fi>.