Test dataset for MacSyFinder (v2) and expected output files

We present here a sample of a genomic dataset, to test MacSyFinder on it (the complete sequence of <em>Vibrio cholerae </em>O1 biovar El Tor str. N16961 chromosome I), along with the expected output files (on the form of compressed folders). <br> The chromosome to annotate is presented as a multi-FASTA file of the proteins ordered as the genes encoding them. An annotation of the protein secretion systems and appendages was run on the genome, using the macsyfinder set of models ("macsy-model") TXSScan, V1.1.1 in the case of these examples. There are two output files offered, the one expected with the "ordered" genome mode of annotation, and the other with the "unordered" mode of genome annotation. The following command lines were used to obtain the output files: <br> First, the genome is downloaded From the present page. Second, the MacSyFinder program is installed. Have a look here for procedure: https://github.com/gem-pasteur/macsyfinder Third, the TXSScan models for annotation of secretion systems are installed. The command line is the following: <br> <em>&gt; macsydata install TXSScan</em> # Install the latest version of TXSScan <br> Finally, MacSyFinder is run on the genome, here using 8 workers for the HMM search ("-w 8" option): In "ordered" mode: <em>&gt; macsyfinder --sequence-db VICH001.B.00001.C001.fasta -o macsyfinder_TXSScan_VICH001_ordered --models TXSScan all --db-type ordered_replicon -w 8</em> # specified output folder: macsyfinder_TXSScan_VICH001_ordered <br> In "unordered" mode: <em>&gt; macsyfinder --sequence-db VICH001.B.00001.C001.fasta -o macsyfinder_TXSScan_VICH001_unordered --models TXSScan all --db-type unordered -w 8</em> # specified output folder: macsyfinder_TXSScan_VICH001_unordered The documentation on the generated output files Can be consulted here. <br>