How to download all the genome sequences (including draft and complete) of a particular genus bacteria available in NCBI?

Question

[Kumar]

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.

[GenoMax]

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

[Kumar]

Dear genomax, I need to download complete genomes along with draft genomes. The cited answer meant for complete genome downloading.

[GenoMax]

The tool linked in @jrj.healey's post can be used to download all genomes available by a command like

ncbi-genome-download --genus "Streptomyces coelicolor" bacteria

Substitute the name shown above for one you are interested in. Use multiple names separated by commas if you need more than one species.

Answer 1

[vmicrobio]

I'll try something like this:

/../edirect/esearch -db nucleotide \
        -query "Xanthomonas[organism] AND genome[title]" \
    | /../edirect/efetch -format fasta > allXanthomonas.fasta

then

makeblastdb -in allXanthomonas.fasta -parse_seqids -dbtype nucl -title xanthomonas -out xanthomonas

good luck

[Kumar]

Dear vmicrobio, Thank you for your answer. But, I could not understand the command given below, /../edirect/esearch -db nucleotide \ -query "Xanthomonas[organism] AND genome[title]" \ | /../edirect/efetch -format fasta > allXanthomonas.fasta is it a script or command, if it so, in which I have to execute this.

The second command seems like a blast command (makeblastdb -in allXanthomonas.fasta -parse_seqids -dbtype nucl -title xanthomonas -out xanthomonas), I need to download all the draft and complete genome sequences from this url https://www.ncbi.nlm.nih.gov/Traces/wgs/?page=1&view=wgs&search=Xanthomonas

[Kumar]

Could you please elaborate your answer and give me more details about the ftp or the programme environment where to execute those commands.

[GenoMax]

@vmicrobio's answer makes use of Entrezdirect. You will need to download that software.