Create README.md

cat/5.3/README.md

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+# CAT
+
+Main tool: [CAT v5.3](https://github.com/dutilh/CAT)
+
+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
+
+
+# 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 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
+```