BASTA

BAsic Sequence Taxonomy Annotation

As the name implies, BASTA assigns taxonomies to sequences or groups of sequences based on the Last Common Ancestor (LCA) of a number of best hits. BASTA can be customised to run on any kind of tabular output (default = blast -outfmt 6) as long as the input file provides values for e-value, percent identity and alignment length. Taxonomies are inferred from NCBI taxonomies based on a 7 level taxonomy.

For detailed usage and installation instructions please visit https://github.com/timkahlke/BASTA/wiki

Citing BASTA

Release v1.2 can be cited as "Kahlke, T. (2018, January 9). Basta 1.2 - Basic Sequence Taxonomy Annotation (Version 1.2). Zenodo. https://doi.org/10.5281/zenodo.1137870"

Requirements

BASTA dependencies and requirements can be installed using the conda environment manager. For installation without conda see installation instructions on the wiki (https://github.com/timkahlke/BASTA/wiki).

Once you have conda installed, do the following:

On OSX/mac:

conda env create -f environment_osx.yml
source activate py27

On Linux:

conda env create -f environment_linux.yml
source activate py27

Now download BASTA and call /bin/basta.

Quick start

Inital Setup

# set up NCBI taxonomy database
./bin/basta taxonomy

# download and set up genbank and uniprot mappings
# NOTE: this might not be needed for you. See Wiki for details
./bin/basta download gb
./bin/basta download prot

Running BASTA

# Infer one LCA for each query sequence of blast against uniprot
./bin/basta sequence BLAST_OUTPUT_FILE BASTA_OUTPUT_FILE prot

# Infer one LCA for the complete blast output file
./bin/basta single BLAST_OUTPUT_FILE prot

# Infer one LCA for each blast output file in a given directory
./bin/basta multiple BLAST_OUTPUT_DIRECTORY BASTA_OUTPUT_FILE prot

Last Common Ancestor algorithm

BASTA supports two algorithms: all and majority

All

If this method is used BASTA reads a given number of best hits for each query sequence and returns the LCA of all sequences (unknown taxonomic levels in database hits are ignored).

Additionally, if the lazy option is used, the user defined minimum number n of hits that is needed to estimate taxonomies will be discarded for sequences with a total hit number <n. Set values for e-value, identity, alignment length etc still apply.

Majority

In this case BASTA determines the LCA based on the LCA of the majority of given best hits. Example: if maximum best hit number is set to 5 and 3 best hits are Bacteria and 2 best hits are Archaea, BASTA returns Bacteria as LCA.

Additional scripts

basta2krona.py

This creates a krona plot (html file) that can be opened in your browser from a basta annotation output file.

./scripts/basta2krona BASTA_OUTPUT_FILE KRONA_HTML_FILE

filter_fasta.py

This script can be used to filter a given fasta file based on BASTA annotations.

./scripts/filter_fasta.py [options] FASTA_FILE FILTERED_OUTPUT_FILE NAME_OF_TAXON BASTA_FILE