From 28df52ced47a860a0c4d95955afaf83c68dfeb3d Mon Sep 17 00:00:00 2001 From: Taylor Paisie Date: Wed, 4 Dec 2024 10:24:00 -0500 Subject: [PATCH] Delete CAT/5.3 directory --- CAT/5.3/README.md | 62 ----------------------------------------------- 1 file changed, 62 deletions(-) delete mode 100644 CAT/5.3/README.md diff --git a/CAT/5.3/README.md b/CAT/5.3/README.md deleted file mode 100644 index d85dffb59..000000000 --- a/CAT/5.3/README.md +++ /dev/null @@ -1,62 +0,0 @@ -# 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 -```