Package: mintyper
Read more about mintyper here:https://academic.oup.com/biomethods/article/6/1/bpab008/6243723Table of contentsIntroductionInstallationStandard usageOutputLicensIntroductionMintyper is a tool designed to quickly estimate a distance matrix from a set of input sequencing reads. It can take both short read from Illumina's sequencing platforms and long reads from Oxford Nanopore's platform.InstallationDependenciesMintyper requires the following dependencies:Python 3.6 or higherKMA (https://bitbucket.org/genomicepidemiology/kma/src/master/)CCphylo (https://bitbucket.org/genomicepidemiology/ccphylo/src/master/)Dependencies installationConda (works on linux only due to KMA conda package)gitclonehttps://bitbucket.org/genomicepidemiology/mintyper.gitcdmintyper
condaenvcreate-fenvironment.yml-nmintyper
condaactivatemintyperManual installation (Linus and MacOS, requires libz-dev installed)gitclonehttps://bitbucket.org/genomicepidemiology/mintyper.gitcdmintyper
python3scripts/install_dependencies.pyMintyper installationUsing pipThe easiest way to install mintyper is using pip:pipinstallmintyperFrom sourcegitclonehttps://bitbucket.org/genomicepidemiology/mintyper.gitcdmintyper
python3setup.pyinstallDatabaseMintyper provides two options: Either the user can give a single fasta file as reference sequence by using the -ref argument, or a whole KMA indexed database can be used with the -db argument.A guide for indexing a given database correctly can be found athttps://bitbucket.org/genomicepidemiology/kma/src/master/A database of complete bacterial genomes can be downloaded with:wgethttps://cge.food.dtu.dk/services/MINTyper/bac_db.tar.gz.Standard usagemintyper--illumina/path/to/illlumina_files/*--nanopore/path/to/nanopore_files/*--db/path/to/database--outputoutput_folder_nameOutputThe output consists of a distance matrix in relaxed phylip format (distmatrix.phy), a list of template candidates (Template_kma_results.spa), the chosen template sequence (template_sequence.fasta), the combined VCF file of all analyzed reads (Combined.vcf.gz), a newick file of the generated phylogenetic tree (outtree.newick), a cluster file (Optional, only outputted if -cluster_length > 0) and a logfile. Additionally, a data folder containing the consensus sequences, the individual VCFs and alignment files is created.CitationMalte B Hallgren, Søren Overballe-Petersen, Ole Lund, Henrik Hasman, Philip T L C Clausen, mintyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads, Biology Methods and Protocols, Volume 6, Issue 1, 2021, bpab008,https://doi.org/10.1093/biomethods/bpab008LicensCopyright(c)2021,MalteHallgren,TechnicalUniversityofDenmarkAllrightsreserved.

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Unlessrequiredbyapplicablelaworagreedtoinwriting,softwaredistributedundertheLicenseisdistributedonan"AS IS"BASIS,WITHOUTWARRANTIESORCONDITIONSOFANYKIND,eitherexpressorimplied.SeetheLicenseforthespecificlanguagegoverningpermissionsandlimitationsundertheLicense.Additional informationAs of April 2023 IQtree and FastTree are no longer supported automatically. If you wish to use these programs, please install them manually and use the distance matrix or multiple alignment as input.