Possibility to download SSU sequences

Ecogenomics / GTDBNCBI

The GTDB provides the software infrastructure for working with a large collection of genomic resources. The major goal of this initiative is to provide a phylogenetically consistent taxonomy for archaea and bacteria.

https://gtdb.ecogenomic.org/

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Possibility to download SSU sequences #40

Closed pchaumeil closed 8 years ago

pchaumeil commented 8 years ago

with the SSU sequences stored now in the database (metadata_ssu table), it would be great to be able to download all of them into a Fasta file.

The format of this Fasta file will be as following:

genome_id|contig_id gtdb_taxonomy sequence

pchaumeil commented 8 years ago

This has been has been implemented and will be available in the next release of GTDB.

The command is : gtdb genomes ssu_export [--output]