Cbcb:Pop-Lab:Bo-Report:metagenomicsData: Difference between revisions
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== Metagenomic Date Sets == | == Metagenomic Date Sets == | ||
The following table shows some metagenomic datasets that are available locally. All the DNA sequences are downloaded directly from NCBI TraceArchive or Short Read Archive without any preprocessing. | The following table shows some metagenomic datasets that are available locally. All the DNA sequences are downloaded directly from NCBI TraceArchive or Short Read Archive without any preprocessing. | ||
<br/><br/> | <br/><br/> | ||
{| class="wikitable" border="1" cellpadding="5" | {| class="wikitable" border="1" cellpadding="5" | ||
|- | |- | ||
! Metagenomics Project | ! Metagenomics Project | ||
! Data Location | ! Data Location | ||
! More Information | ! More Information | ||
|- | |- | ||
Line 21: | Line 21: | ||
|- | |- | ||
| Metagenomic Water Samples from Rita Colwell | | Metagenomic Water Samples from Rita Colwell | ||
| /fs/szdata/metagenomes/reads/freshwaterUMIGS/freshwaterUMIGS1.fasta /fs/szdata/metagenomes/reads/freshwaterUMIGS/freshwaterUMIGS2.fasta | | /fs/szdata/metagenomes/reads/freshwaterUMIGS/freshwaterUMIGS1.fasta <br> /fs/szdata/metagenomes/reads/freshwaterUMIGS/freshwaterUMIGS2.fasta | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33243 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33243] | ||
|- | |- | ||
| | | Gut metagenomes collected from 13 healthy individuals (Japan) | ||
| | | All 13 fasta files (with fasta suffix) in this directory: /fs/szdata/metagenomes/reads/gutJapan/F1S.fasta | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28117 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28117] | ||
|- | |- | ||
| | | Human Gut Microbiome from Obese and Lean Twins | ||
| | | All 18 fasta files (with fasta suffix) in this directory: /fs/szdata/metagenomes/reads/gutTwin | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32089 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32089] | ||
|- | |- | ||
| | | Metagenome from Lake Washington | ||
| | | All 5 fasta files in this directory: /fs/szdata/metagenomes/reads/lakeWash | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30541 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30541] | ||
|- | |- | ||
| | | Sampling of Marine Metagenomes project at Broad Institute | ||
| | | All 7 fasta files in this directory: /fs/szdata/metagenomes/reads/marineBroad | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30501 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30501] | ||
|- | |- | ||
| | | Marine Metagenome from Coastal Waters project at Plymouth Marine Laboratory | ||
| | | /fs/szdata/metagenomes/reads/marinePlymouth/plyM.fasta <br> /fs/szdata/metagenomes/reads/marinePlymouth/plyT.fasta | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28969 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28969] | ||
|- | |- | ||
| | | Metagenomics of the Human Intestinal Tract, MetaHit. | ||
| | | All 5 fasta files in this directory: /fs/szdata/metagenomes/reads/metahit | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32811 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32811] | ||
|- | |- | ||
| | | Metagenome isolated from Guerrero Negro hypersaline microbial mat in Mexico | ||
| | | All 10 fasta files in this directory: /fs/szdata/metagenomes/reads/microbialMat | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29795 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29795] | ||
|- | |- | ||
| | | Micro-Obes human intestinal tract metagenome project. | ||
| | | All 5 fasta files in this dicrectory: /fs/szdata/metagenomes/reads/microobes | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33303 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33303] | ||
|- | |- | ||
| | | Enhanced biological phosphorus removal (EBPR) sludge community. | ||
| | | /fs/szdata/metagenomes/reads/sludge/sludgeOZ.fasta <br> /fs/szdata/metagenomes/reads/sludge/sludgeUS.fasta | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=17663 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=17663] | ||
|- | |- | ||
| | | Waseca County Farm Soil Metagenome | ||
| | | /fs/szdata/metagenomes/reads/soilWaseca/soilWaseca.fasta | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13699 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13699] | ||
|- | |- | ||
| | | Wastewater Metagenome MallardCreek032007AerobicBasin | ||
| | | /fs/szdata/metagenomes/reads/wasteWater/wasteWater.fasta | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29421 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29421] | ||
|- | |- | ||
| | | Whale Fall Metagenome | ||
| | | /fs/szdata/metagenomes/reads/whale/bone.fasta <br> /fs/szdata/metagenomes/reads/whale/microbialMat.fasta <br> /fs/szdata/metagenomes/reads/whale/ribBone.fasta | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13700 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13700] | ||
|- | |- | ||
| | | Yellowstone Bison Hot Spring Metagenome | ||
| | | /fs/szdata/metagenomes/reads/ys/ysBisonP1.fasta <br> /fs/szdata/metagenomes/reads/ys/ysBisonP3.fasta <br> /fs/szdata/metagenomes/reads/ys/ysBisonP4.fasta <br> /fs/szdata/metagenomes/reads/ys/ysBisonP5.fasta <br> | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=34795 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=34795] | ||
|- | |- | ||
| | | Global Ocean Sampling Expedition Metagenome | ||
| | | All 8 fasta files in this directory: /fs/szdata/metagenomes/reads/marineGlobe | ||
| | | [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13694 http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13694] | ||
|} | |} |
Latest revision as of 16:20, 31 August 2009
Metagenomic Date Sets
The following table shows some metagenomic datasets that are available locally. All the DNA sequences are downloaded directly from NCBI TraceArchive or Short Read Archive without any preprocessing.
Metagenomics Project | Data Location | More Information |
---|---|---|
UBA Acid Mine Drainage Biofilm Metagenome | /fs/szdata/metagenomes/reads/acidMine/acidMineUba.fasta | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=18537 |
5-Way (CG) Acid Mine Drainage Biofilm Metagenome | /fs/szdata/metagenomes/reads/acidMine/acidMineCg.fasta | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13696 |
Antarctica Aquatic Microbial Metagenome | /fs/szdata/metagenomes/reads/antarctica/antarctica.fasta | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33179 |
Metagenomic Water Samples from Rita Colwell | /fs/szdata/metagenomes/reads/freshwaterUMIGS/freshwaterUMIGS1.fasta /fs/szdata/metagenomes/reads/freshwaterUMIGS/freshwaterUMIGS2.fasta |
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33243 |
Gut metagenomes collected from 13 healthy individuals (Japan) | All 13 fasta files (with fasta suffix) in this directory: /fs/szdata/metagenomes/reads/gutJapan/F1S.fasta | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28117 |
Human Gut Microbiome from Obese and Lean Twins | All 18 fasta files (with fasta suffix) in this directory: /fs/szdata/metagenomes/reads/gutTwin | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32089 |
Metagenome from Lake Washington | All 5 fasta files in this directory: /fs/szdata/metagenomes/reads/lakeWash | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30541 |
Sampling of Marine Metagenomes project at Broad Institute | All 7 fasta files in this directory: /fs/szdata/metagenomes/reads/marineBroad | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=30501 |
Marine Metagenome from Coastal Waters project at Plymouth Marine Laboratory | /fs/szdata/metagenomes/reads/marinePlymouth/plyM.fasta /fs/szdata/metagenomes/reads/marinePlymouth/plyT.fasta |
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=28969 |
Metagenomics of the Human Intestinal Tract, MetaHit. | All 5 fasta files in this directory: /fs/szdata/metagenomes/reads/metahit | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=32811 |
Metagenome isolated from Guerrero Negro hypersaline microbial mat in Mexico | All 10 fasta files in this directory: /fs/szdata/metagenomes/reads/microbialMat | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29795 |
Micro-Obes human intestinal tract metagenome project. | All 5 fasta files in this dicrectory: /fs/szdata/metagenomes/reads/microobes | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=33303 |
Enhanced biological phosphorus removal (EBPR) sludge community. | /fs/szdata/metagenomes/reads/sludge/sludgeOZ.fasta /fs/szdata/metagenomes/reads/sludge/sludgeUS.fasta |
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=17663 |
Waseca County Farm Soil Metagenome | /fs/szdata/metagenomes/reads/soilWaseca/soilWaseca.fasta | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13699 |
Wastewater Metagenome MallardCreek032007AerobicBasin | /fs/szdata/metagenomes/reads/wasteWater/wasteWater.fasta | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=29421 |
Whale Fall Metagenome | /fs/szdata/metagenomes/reads/whale/bone.fasta /fs/szdata/metagenomes/reads/whale/microbialMat.fasta /fs/szdata/metagenomes/reads/whale/ribBone.fasta |
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13700 |
Yellowstone Bison Hot Spring Metagenome | /fs/szdata/metagenomes/reads/ys/ysBisonP1.fasta /fs/szdata/metagenomes/reads/ys/ysBisonP3.fasta /fs/szdata/metagenomes/reads/ys/ysBisonP4.fasta /fs/szdata/metagenomes/reads/ys/ysBisonP5.fasta |
http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=34795 |
Global Ocean Sampling Expedition Metagenome | All 8 fasta files in this directory: /fs/szdata/metagenomes/reads/marineGlobe | http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Retrieve&dopt=Overview&list_uids=13694 |