Cbcb:Pop-Lab:Bo-Report:metagenomicsData
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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 |