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447 results for “Binning”
Bin-assembled Escherichia coli genomes from a study in Punjab, Pakistan
<h2>Bin-assembled <em>Escherichia coli</em> genomes from Punjab, Pakistan</h2> <p>These assemblies are a part of a cross-sectional study conducted in Punjab, Pakistan aimed at investigating <em>E. coli</em> colonisation diversity in healthy carriage with the use of CLED enrichment plates.</p> <h3><strong>About</strong></h3> <h4><strong>Version history</strong></h4> <p><strong>v0.1.1 (current version)</strong></p> <ul> <li>Added reference to the study.</li> </ul> <p><strong>v0.1.0</strong></p> <ul> <li>Added brief description with a few missing parts.</li> </ul> <h4><strong>Distribution</strong></h4> <p>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.</p> <h4><strong>Citation</strong></h4> <p>Khawaja, T., Mäklin, T., Kallonen, T. et al. Deep sequencing of <em>Escherichia coli</em> exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nature Communications 15, 5196 (2024). <a href="https://doi.org/10.1038/s41467-024-49591-5">https://doi.org/10.1038/s41467-024-49591-5</a></p> <h3><strong>Methods briefly</strong></h3> <h4><strong>Species identification</strong></h4> <p>Sequencing data from the ENA project <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB36642">PRJEB36642</a> was error-corrected with <a href="https://github.com/opengene/fastp">fastp</a> and pseudoaligned with <a href="https://github.com/algbio/themisto">Themisto</a> against a species-level index (available from <a href="https://doi.org/10.5281/zenodo.6656881">https://doi.org/10.5281/zenodo.6656881</a>). Reads were assigned to species using the <a href="https://doi.org/10.1099%2Fmgen.0.000691">mSWEEP/mGEMS pipeline</a> as described in <a href="https://www.nature.com/articles/s41467-022-35178-5">https://www.nature.com/articles/s41467-022-35178-5</a>.</p> <h4><strong>Lineage identification</strong></h4> <p>Read from the species-level bins were again pseudoaligned with Themisto against an <em>E. coli</em> index (will be made available in a later version). Lineage-level assignment was performed using mSWEEP and mGEMS at the level of <a href="https://genome.cshlp.org/content/29/2/304">PopPUNK</a> sequence clusters. The created bins were screened with <a href="https://github.com/tmaklin/coreutils_demix_check">demix_check</a> and bins that received a score of 1 or 2 were kept. Data in the kept bins were assembled with <a href="https://github.com/tseemann/shovill">shovill</a> and the bin-assembled genomes (BAGs) were quality controlled with <a href="https://genome.cshlp.org/content/25/7/1043">checkm</a> for >= 90% completeness and <= 10% contamination. Finally, BAGs shorter than 4 Mb or longer than 6 Mb were removed.</p> <h3><strong>Contact</strong></h3> <p>Tommi Mäklin <tommi'at'maklin.fi>.</p>
BBS phase 1 & phase 2 high quality E. coli bin assembled genomes
<p>1,402 <em>Escherichia coli</em> bin assembled genomes derived from the metagenome data collected as part of the <a href="https://www.ucl.ac.uk/global-health/research/a-z/baby-biome-study">BabyBiome study (BBS)</a> phase 1 & phase 2.</p> <p>The data in this upload was first published as part of "<em>Group 2 and 3 ABC-transporter dependant K-antigen loci contribute significantly to variation in the invasive potential of Escherichia coli"</em> (Gladstone et al. 2024, to be released).</p> <h2>Files</h2> <p>Assembly data:</p> <ul> <li>BBS_E_coli_BAGs.tar: Archive containing sequences of the 1,402 bin assembled genomes.</li> <li>BBS_E_coli_metadata.tsv: Table linking the sequence assemblies to the subject data.</li> </ul> <p>Capsule predictions:</p> <ul> <li>BBS_E_coli_Kaptive_output.csv: Capsule predictions for all sequence data.</li> <li>BBS_E_coli_deduplicated_sequences_IDs.txt: Filenames for assemblies that constitute the 873 deduplicated sequences analysed in Gladstone et al. 2024.</li> </ul> <p>Quality control data:</p> <ul> <li>BBS_E_coli_demix_check_scores.tsv: Output from demix_check for the sequence assemblies.</li> <li>BBS_E_coli_checkm_results.tsv: Output from checkm.</li> <li>BBS_E_coli_gunc_results.tsv: Output from gunc.</li> </ul> <h2>Methods</h2> <h3>Bin assembled genomes</h3> <p>Source data:</p> <ul> <li>BBS phase 1: <a href="https://doi.org/10.1038/s41586-019-1560-1">Shao et al. 2019</a></li> <li>BBS phase 2: <a href="https://doi.org/10.1038/s41564-024-01804-9">Shao et al. 2024</a></li> </ul> <p>The data was produced using the mSWEEP and mGEMS pipeline (<a href="https://doi.org/10.12688/wellcomeopenres.15639.2">Mäklin et al. 2020</a> & <a href="https://doi.org/10.1099/mgen.0.000691">Mäklin et al. 2021</a>) following the steps described in <a href="https://doi.org/10.1038/s41467-024-49591-5">Khawaja, Mäklin, Kallonen, et al. 2024</a>.</p> <h3>Quality control</h3> <p>The BAGs in this upload were filtered with demix_check (<a href="https://github.com/harry-thorpe/demix_check">https://github.com/harry-thorpe/demix_check</a>) and only those with a quality score 1 or 2 are included. For the capsule type annotations, contigs shorter than 5,000bp were removed but the short contigs are still present in the uploaded files). Further QC data is available from checkm (<a href="https://genome.cshlp.org/content/25/7/1043.short">Parks et al. 2015</a>) and gunc (<a href="https://link.springer.com/article/10.1186/s13059-021-02393-0">Orakov et al. 2022</a>) results.</p> <h3>Multilocus sequence typing</h3> <p>Sequence type (ST) was determined using fastmlst (<a href="https://journals.sagepub.com/doi/10.1177/11779322211059238">Guerrero-Araya et al. 2021</a>) with the `ecoli#1` database.</p> <h3>PopPUNK clustering</h3> <p>Sequence clusters (SC) correspond to the database available from <a href="https://zenodo.org/records/12528310">https://zenodo.org/records/12528310</a> and were created using PopPUNK (<a href="https://genome.cshlp.org/content/29/2/304.short">Lees et al. 2019</a>). Construction is described in <a href="https://doi.org/10.1038/s41467-024-49591-5">Khawaja, Mäklin, Kallonen, et al. 2024</a>.</p> <h3>Capsule type annotations</h3> <p>The capsule type annotations were created using Kaptive (<a href="https://doi.org/10.1099/mgen.0.000800">Lam et al. 2022</a>) with an <em>E. coli</em> specific database available from <a href="https://github.com/rgladstone/EC-K-typing">https://github.com/rgladstone/EC-K-typing</a> and described in Gladstone et al. 2024.</p>
BGQNAPv1.0: A summer macronutrients binned data set for the Northern Antarctic Peninsula, Southern Ocean
<p>We compiled a time series spanning the period from 1996 to 2019 of the seawater hydrographic variables conservative temperature (<sup>o</sup>C), absolute salinity (g kg<sup>­–1</sup>) and dissolved oxygen (μmol kg<sup>­–1</sup>), and the macronutrients DIN (nitrate + nitrite + ammonium), phosphate, and silicic acid (μmol kg<sup>­–1</sup>). The study area covered the northern Antarctic Peninsula regions including the Gerlache Strait and the western, central, and eastern basins of Bransfield Strait. Most data (~90%) were obtained from the Brazilian High Latitude Oceanography Group (GOAL; http://goal.furg.br/) from austral summer field campaigns (January-March). In some years (1996, 2005, 2006, 2010, 2011) we used hydrographic and macronutrient data from GLODAP 2020 (Olsen et al., 2020) along the NAP and exceptionally for 1996 we used data available from December 1995 to February 1996 (the FRUELA cruises, García et al., 2022; Álvarez et al., 2002). Details on the sampling and analysis of macronutrient data obtained from GLODAP dataset can be accessed on the OCADS platform (<a href="https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system-portal/">https://www.ncei.noaa.gov/access/ocean-carbon-acidification-data-system-portal/</a>).</p> <p>About 97% of the DIN data were composed of nitrate, followed by ammonium (2%) and nitrite (1%). Therefore, in some cases (11% of all data), we considered DIN as the nitrate concentration, when no nitrite and/or ammonium data were available. Discrete seawater samples were collected at irregular depth intervals from surface (5 m) to deep waters (at approximately 15 m from the bottom). We averaged the parameters for each region at regular depth intervals from the surface to the bottom (i.e., 0, 25, 50, 75, 100, 250, 500, 750, 1000, 1250, 1500, 1750, 2000, 2500 m) to obtain an averaged summer profile for each year.</p> <p>All sampling and analyses information of the hydrographic and macronutrients are detailed in Kerr et al. (2018), Mata et al. (2018), Dotto et al. (2021) and Costa et al. (2020), and references therein.</p>
December 2002 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Doboy Sound transect
Two hydrographic surveys were performed December 10, 2002, along an east-to-west transect through Doboy Sound near Sapelo Island, Georgia (Doboy Sound Transect, GCE-DB). Vertical CTD profiles were collected at approximately 2km intervals from -2km to 12km along the transect during low tide and high tide conditions. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
December 2002 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Intracoastal Waterway transect
Three hydrographic surveys were performed from December 10 to December 11, 2002, along the Intracoastal Waterway between the Altamaha River south of Wolf Island and Sapelo Sound (Intracoastal Waterway Transect, GCE-IC). Vertical CTD profiles were collected at various intervals from -15km to 29km along the transect during various tidal regimes. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
December 2002 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Altamaha River transect
Four hydrographic surveys were performed on December 11, 2002, along an east-to-west transect up the Altamaha River in Georgia (Altamaha River Transect, GCE-AL). Vertical CTD profiles were collected at 1-2km intervals from the -2km to 28km upriver along the transect during low and high tidal regimes. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
December 2002 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Inner Marsh transect
One hydrographic survey was performed on December 11, 2002, along the Darien River, North River, and north channel of the Altamaha River (Inner Marsh Transect, GCE-IM). Vertical CTD profiles were collected at various nominal stations along the transect under a low water tidal regime (late ebb to early flood tide). Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
December 2002 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Sapelo River transect
Three hydrographic surveys were performed on December 12, 2002, along a transect from Sapelo Sound up the Sapelo River to Eulonia, Georgia (Sapelo River Transect, GCE-SP). Vertical CTD profiles were collected at approximately 2km intervals from 0km to 36km during low and high tidal regimes. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
March 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Altamaha River transect
Nine hydrographic surveys were performed from March 26 to March 31, 2003, along an east-to-west transect up the Altamaha River in Georgia (Altamaha River Transect, GCE-AL). Vertical CTD profiles were collected at 1-2km intervals from the -4km to 24km upriver along the transect during various tidal regimes. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
March 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Intracoastal Waterway transect
Four hydrographic surveys were performed from March 26 to March 20, 2003, along the Intracoastal Waterway between the Altamaha River south of Wolf Island and Sapelo Sound (Intracoastal Waterway Transect, GCE-IC). Vertical CTD profiles were collected at various intervals from -19km to 12km along the transect during various tidal regimes. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
March 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Duplin River transect
Two hydrographic surveys were performed on March 26 and March 28, 2003, along an south-to-north transect up the Duplin River on Sapelo Island, Georgia (Duplin River Transect, GCE-DP). Vertical CTD profiles were collected at various nominal stations along the transect during various tidal conditions. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
March 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Inner Marsh transect
One hydrographic survey was performed on March 27, 2003, along the Darien River, North River, and north channel of the Altamaha River (Inner Marsh Transect, GCE-IM). Vertical CTD profiles were collected at various nominal stations along the transect under a low water tidal regime (flood tide). Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
March 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Sapelo River transect
Three hydrographic surveys were performed from March 27 to March 28, 2003, along a transect from Sapelo Sound up the Sapelo River to Eulonia, Georgia (Sapelo River Transect, GCE-SP). Vertical CTD profiles were collected at approximately 2km intervals from 0km to 36km during low and high tidal regimes. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
March 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Doboy Sound transect
Three hydrographic surveys were performed from March 28 to March 29, 2003 , along an east-to-west transect through Doboy Sound near Sapelo Island, Georgia (Doboy Sound Transect, GCE-DB). Vertical CTD profiles were collected at approximately 2km intervals from 0km to 12.7km along the transect during low tide and high tide conditions. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
June 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Doboy Sound transect
Two hydrographic surveys were performed on June 18, 2003, along an east-to-west transect through Doboy Sound near Sapelo Island, Georgia (Doboy Sound Transect, GCE-DB). Vertical CTD profiles were collected at approximately 2km intervals from -2km to 12km along the transect during low tide and high tide conditions. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
June 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Intracoastal Waterway transect
Two hydrographic surveys were performed from June 18 to June 19, 2003, along the Intracoastal Waterway between the Altamaha River south of Wolf Island and Sapelo Sound (Intracoastal Waterway Transect, GCE-IC). Vertical CTD profiles were collected at various intervals from 0km to 23km along the transect during various tidal regimes. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
June 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Altamaha River transect
Three hydrographic surveys were performed on June 19, 2003, along an east-to-west transect up the Altamaha River in Georgia (Altamaha River Transect, GCE-AL). Vertical CTD profiles were collected at 2km intervals from the -4km to 24km upriver along the transect during various tidal regimes. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
June 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Duplin River transect
Two hydrographic surveys were performed on June 17 and June 18, 2003, along an south-to-north transect up the Duplin River on Sapelo Island, Georgia (Duplin River Transect, GCE-DP). Vertical CTD profiles were collected at various nominal stations along the transect during various tidal conditions. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
June 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Inner Marsh transect
One hydrographic survey was performed on June 19, 2003, along the Darien River, North River, and north channel of the Altamaha River (Inner Marsh Transect, GCE-IM). Vertical CTD profiles were collected at various nominal stations along the transect under a low water tidal regime (flood tide). Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
June 2003 bin-averaged CTD profiles for the Georgia Coastal Ecosystems Sapelo River transect
Three hydrographic surveys were performed on June 20, 2003, along a transect from Sapelo Sound up the Sapelo River to Eulonia, Georgia (Sapelo River Transect, GCE-SP). Vertical CTD profiles were collected at 3-4km intervals from -12km to 36km during low and high tidal regimes. Conductivity, temperature, pressure and optical backscatter were measured, and depth, salinity and sigma-t were calculated for each profile. Data values collected on the upcast were deleted, and the remaining data were averaged within 0.5m depth bins and interpolated to produce a smooth profile for contouring. This data set was collected as part of the Georgia Coastal Ecosystems LTER quarterly hydrographic monitoring program.
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