The bioBakery help forum

Synthetic human gut metagenome

Microbial community profiling HUMAnN
#1

Hey guys,

To start with, I hope I am posting this in the appropriate place, if not please feel free to redirect me!

I was wondering if I could find out which exact reference genomes were used to create the synthetic human gut data from the HUMAnN2 paper (available at http://huttenhower.sph.harvard.edu/humann2_data/synthetic_packaging/synthetic_dna_human_gut.tar.gz). The info in the paper explains how the synthetic data was made, but I was unable to find any accession numbers etc.

Any help would be gratefully received,

Thank you in advance,
Becky

#2

Here you go:

g__Alistipes.s__Alistipes_onderdonkii                GCF_000374505
g__Alistipes.s__Alistipes_putredinis                 GCF_000154465
g__Alistipes.s__Alistipes_shahii                     GCF_000210575
g__Bacteroides.s__Bacteroides_caccae                 GCF_000273725
g__Bacteroides.s__Bacteroides_cellulosilyticus       GCF_000158035
g__Bacteroides.s__Bacteroides_dorei                  GCF_000273035
g__Bacteroides.s__Bacteroides_massiliensis           GCF_000373085
g__Bacteroides.s__Bacteroides_ovatus                 GCF_000154125
g__Bacteroides.s__Bacteroides_stercoris              GCF_000413395
g__Bacteroides.s__Bacteroides_thetaiotaomicron       GCF_000011065
g__Bacteroides.s__Bacteroides_uniformis              GCF_000273785
g__Bacteroides.s__Bacteroides_vulgatus               GCF_000403235
g__Barnesiella.s__Barnesiella_intestinihominis       GCF_000296465
g__Dialister.s__Dialister_invisus                    GCF_000160055
g__Eubacterium.s__Eubacterium_rectale                GCF_000209955
g__Faecalibacterium.s__Faecalibacterium_prausnitzii  GCF_000166035
g__Parabacteroides.s__Parabacteroides_distasonis     GCF_000012845
g__Parabacteroides.s__Parabacteroides_merdae         GCF_000154105
g__Prevotella.s__Prevotella_copri                    GCF_000157935
g__Ruminococcus.s__Ruminococcus_bromii               GCF_000209875
#4

@BioMickWatson Did you mean to post this on the thread you started? I just replied there with the gold standard information.

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