Question: How to download all the genome sequences (including draft and complete) of a particular genus bacteria available in NCBI?
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gravatar for Dineshkumar K
10 days ago by
Kasaragod, Kerala, India
Dineshkumar K0 wrote:

I would like to conduct a comparative genome analysis of Xanthomonads. For which, I have been downloading all the available Xanthomonas genome (including draft and complete genome fasta format file) in NCBI of all Xanthomonas strains. As of now, I found more than 2000 genomes are available in NCBI bioproject and NCBI Sequence set database (https://www.ncbi.nlm.nih.gov/Traces/wgs/?page=1&view=wgs&search=Xanthomonas). Downloading one by by one genome is too tedious . Hence, please suggest me any shortcut or easy way to do the same. However, I could only download the summary of all the available genome sequences in xls or csv format.

Please note that, I have already tried with NCBI Assembly database and NCBI Genome Database, But I could not find all the draft and complete genome sequences, which I found in NCBI sequence set browser and NCBI bioproject (please refer the below link) https://www.ncbi.nlm.nih.gov/Traces/wgs/?page=1&view=wgs&search=Xanthomonas

I have tried with biomartr R package, wherein, I could find only NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, NCBI nt, Ensembl, Ensembl Genome databases. However I could not find my draft genome of interest in the above mentioned databases, which I found at NCBI Bioproject and NCBI sequence set browser mentioned above.

I am looking forward for your valid suggestion for the same.

ADD COMMENTlink written 10 days ago by Dineshkumar K0
1

Use the tool in this answer : A: How to download all the complete genomes of a bacterium (eg E. coli, Mycobacteri

ADD REPLYlink modified 10 days ago • written 10 days ago by genomax60k
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