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CAT

Main tool: CAT

Code repository: https://github.com/MGXlab/CAT_pack

Basic information on how to use this tool:

  • executable: CAT_pack
  • help: --help
  • version: --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/MGXlab/CAT_pack

Testing 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_pack 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_pack contigs -c test/burk_wgs_pos_ctrl.fa \
    -d db_tests/db \
    -t db_tests/tax

# Running BAT on a set of MAGs
CAT_pack bins -b test/GN02_MAG_IV_B_1-contigs.fa \
    -d db_tests/db \
    -t db_tests/tax