Main tool: CAT v5.3
Code repository: https://github.com/dutilh/CAT
Basic information on how to use this tool:
- executable: |
usage: CAT (prepare | contigs | bin | bins | add_names | summarise) [-v / --version] [-h / --help]
Run Contig Annotation Tool (CAT) or Bin Annotation Tool (BAT).
Required choice:
download Download and preprocess data from NCBI nr or GTDB.
prepare Construct database files.
contigs Run CAT.
bins Run BAT.
add_names Add taxonomic names to CAT or BAT output files.
summarise Summarise a named CAT or BAT classification file.
Optional arguments:
-v, --version Print version information and exit.
-h, --help Show this help message and exit.
- help:
CAT --help - version:
CAT --version - description: |
Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies
Full documentation: https://github.com/dutilh/CAT
# Download test data
wget -nv --no-check-certificate https://raw.githubusercontent.com/taylorpaisie/docker_containers/main/checkm2/1.0.2/burk_wgs.fa -O burk_wgs_pos_ctrl.fa
wget -nv --no-check-certificate https://merenlab.org/data/refining-mags/files/GN02_MAG_IV_B_1-contigs.fa -O GN02_MAG_IV_B_1-contigs.fa
# Prepare testing database
RUN mkdir -p db_tests && \
gzip -d /CAT/tests/data/prepare/small.fa.gz && \
CAT prepare --db_fasta /CAT/tests/data/prepare/small.fa \
--acc2tax /CAT/tests/data/prepare/prot2acc.txt \
--names /CAT/tests/data/prepare/names.dmp \
--nodes /CAT/tests/data/prepare/nodes.dmp \
--db_dir db_tests/
# Use CAT and BAT for taxonomic classification for both best datasets
# Running CAT on contigs
CAT contigs -c test/burk_wgs_pos_ctrl.fa \
-d db_tests/db \
-t db_tests/tax
# Running BAT on a set of MAGs
CAT bins -b test/GN02_MAG_IV_B_1-contigs.fa \
-d db_tests/db \
-t db_tests/tax