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retrieving entire genomic sequence contents of a database

Hi all, I'm trying to download all bacterial genomes from ensembl so I can further mine them for bacteriocin gene clusters. However I've been struggling and was hoping someone could advise? Any time I attempt the wget command on the index URL below I get results like "index.html". I've also tried things like wget ftp://ftp.bacteria.ensembl.org/species but no luck.

Can someone please advise on the steps I should take in order to be able to pull all genomic sequences from a database from the command line via ftp, preferably in gbk, gff, or fasta format.

Any help is greatly appreciated!

genomes mining database ftp ensembl
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updated by Ben Moore Ben Moore • written by saundythe8th • saundythe8th

2 answers

There is a script here that does massive genome data download, but from NCBI. For example, this command will download all RefSeq complete bacterial genomes:

genome_updater.sh -g "bacteria" -d "refseq" -l "Complete Genome" -f "genomic.fna.gz" -o "bac_refseq" -t 20

A small command-line change will let you download all GenBank genomes if you wish, and include even those (meta)genomes that may not be complete.

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written by Mensur Dlakic Mensur Dlakic

Hi sandrewsaunderson,

If you are keen to use Ensembl for this task, it's important to remember that the bacterial files are stored in collections on the FTP site. E.g: http://ftp.ensemblgenomes.org/pub/bacteria/release-51/fasta/

This may be where you have encountered problems with your download.

Best wishes

Ben Ensembl Helpdesk

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written by Ben Moore Ben Moore

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