Home

BASTA - BAsic Sequence Taxonomy Annotation

BASTA is a command-line tool written in python that was developed to enable a basic taxonomy annotation based on a Last Common Ancestor algorithm similar to the one implemented in MEGAN. BASTA allows annotation of any kind of sequence or group of sequences, e.g., contigs, protein and gene sequences, reads, contig bins etc based on the NCBI taxonomy and tabular sequence comparison output. Additionally, BASTA provides utility scripts for taxonomy visualisation using Krona, fasta file filtering and others.

How does it work ?

Given a sequence comparison file, e.g. a tabular blast output file of query sequences, BASTA takes the best X hits (default = all) of each query sequence and determines the Last Common Ancestor of the hit taxonomies. The definition of best hit can be adjusted using e-value, alignment length and percent identity of each hit.

Accession vs GI numbers

In contrast to other tools BASTA uses NCBI accession numbers and not Gi-numbers to determine taxon_ids of each hit sequence. Thus the discontinuation of Gi-numbers as recently announced by the NCBI will not affect BASTA.

Supported sequence comparison tools

Per default BASTA expects tabular sequence comparison files in blast output, i.e., blast outfmt option set to 6. However, BASTA can easily be customised to use any tabular output as long as each hit-line contains values for the query and subject sequence's name, e-value, alignment length and percent identity.

Supported databases

As long as the hit or matching sequences' names include an NCBI accession number BASTA will be able to annotate these. BASTA provides functions to download and process mapping files for accession-to-taxonid for all NCBI databases such as protein sequences (e.g. Uniprot accession numbers), nucleotide sequences (e.g. Genbank accession numbers), NCBI's whole genome sequence accession numbers, Protein Database (PDB) accession numbers and others.