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
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