Hi,
I'm new to bioinformatics and have a problem with getting taxonomic information for my contig database.
Currently I have a file that has all the contigs IDs with their taxonomic assignment to the species level as the output of an annotation pipeline. However, for another analysis, I want to group all the contigs by their higher taxonomic level, like family or order. How can I retrieve the higher taxonomic information through the species names?
Does anyone know a tool that can map the species name to NCBI taxonomy database and output the higher taxonomic level name information?
For example, when the input is Escherichia coli, the output would be: (in a table), Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Escherichia.
Thanks.
I'm new to bioinformatics and have a problem with getting taxonomic information for my contig database.
Currently I have a file that has all the contigs IDs with their taxonomic assignment to the species level as the output of an annotation pipeline. However, for another analysis, I want to group all the contigs by their higher taxonomic level, like family or order. How can I retrieve the higher taxonomic information through the species names?
Does anyone know a tool that can map the species name to NCBI taxonomy database and output the higher taxonomic level name information?
For example, when the input is Escherichia coli, the output would be: (in a table), Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacteriales, Enterobacteriaceae, Escherichia.
Thanks.
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