Hi,
I have a question about the metaphlan4.
Are the SGB genome sequences available for use/download? Actually in the metaphlAn github it provided SGB download link. But it only about the human SGB. I need SGB from non-human.
Or, Can I get the genome sequence which was used to make a synthetic metagenome data in metaphlan4 (Index of /biobakery4/synthetic_metagenomes)?
Thank you
Hi @kim
Unfortunately, we do not have available the sequences of the MAGs used to build the metaphlan 4 database nor the synthetic metagenomes. Only the reference genomes are available to download (you can find the GCA ids in the Table S1 of the preprint.
Hello Aitor.
I was wondering if it was still the case now ?
I am trying to download the genomic sequences of the following bins:
SGB69890 BandlaA_2020__GLV1604238 Bacteroidetes_CFGB46559
SGB62327 NayfachS_2020__GEM_3300025457__bin.5 Clostridiaceae_GGB47679
SGB56606 NayfachS_2020__GEM_3300025619__bin.13 Proteobacteria_CFGB13676
But I cannot find them, either in The 4,930 SGBs’ representatives from
or in lifebit portal https://opendata.lifebit.ai/table/sgb.
However, there are definitely some metagenomic bin sequences in the lifebit portal, so I am a bit confused…
Am i looking at the wrong place ?
Thank you very much in advance for your help.
best
lorrie
Hi @lorrie_maccario
Unfortunatelly, it is, the only MAGs available in lifebit are those from the original SGB publication Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle - ScienceDirect
Hi @lorrie_maccario.
I recently had the same question.
Nayfach et al. deposited their MAGs on the Join Genome Institute Genome Portal (Index of /GEM/genomes).
Bandla et al. deposited their MAGs on figshare (910 metagenome-assembled genomes from the phytobiomes of three urban-farmed leafy Asian greens) in the glv_mags_fasta.tar.gz archive.
Thank you for your answer @aitor.blancomiguez
and thank you very much for your input @Anthony_McLean , that is really helpful !