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    34 repositories

    • ConFindr

      Public
      Intra-species bacterial contamination detection
      Python
      •
      MIT License
      •8•24•8•1•Updated Jan 29, 2025Jan 29, 2025

    • COWBAT

      Public
      CFIA OLC Workflow for Bacterial Assembly and Typing
      Python
      •
      MIT License
      •5•4•1•0•Updated Jan 8, 2025Jan 8, 2025

    • OLCTools

      Public
      Python package for commonly used tools at OLC.
      Python
      •
      MIT License
      •3•2•2•0•Updated Dec 12, 2024Dec 12, 2024

    • conda_recipes

      Public
      MIT License
      •0•1•0•0•Updated Nov 19, 2024Nov 19, 2024

    • STxDB

      Public
      This repository contains curated virulence stx genes from Ecoli genomes
      0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • BaitCapture

      Public
      A Nextflow workflow for processing data obtained from targeted resistome bait-capture sequencing
      Nextflow
      •
      MIT License
      •0•2•1•0•Updated Sep 13, 2024Sep 13, 2024

    • redmine-docs

      Public
      User documentation for OLC Redmine instance
      HTML
      •
      MIT License
      •0•0•0•0•Updated Aug 15, 2024Aug 15, 2024

    • PoreSippR-GUI

      Public
      GUI for PoreSippR
      Python
      •0•0•0•0•Updated Aug 7, 2024Aug 7, 2024

    • kma_geneseekr_parser

      Public
      This parser is used to compare kma and geneseekr output of two colums seqid and stx genes and user have to provide mapping file
      Python
      •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

    • Poresippr_code

      Public
      Poresippr python code for analysing the stx genes
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 25, 2024Jul 25, 2024

    • AlleleFinder

      Public
      A suite of tools, written in Python, designed for the discovery, sequence typing, and profiling the stx alleles in Shiga toxin-producing E. coli
      Python
      •
      MIT License
      •0•1•0•1•Updated Jul 15, 2024Jul 15, 2024

    • olc_genomics_portal

      Public
      Source for OLC's Genomics Portal
      JavaScript
      •1•3•13•16•Updated May 22, 2024May 22, 2024

    • StrainChoosr

      Public
      🌴 Choose the most diverse possible set of strains from a phylogenetic tree
      Python
      •
      MIT License
      •0•0•1•1•Updated May 16, 2024May 16, 2024

    • salmonella_accessoryscript

      Public
      This python script takes the bunch of fasta files like 5000k or so in one single directory and it moves into multiple subdirectories ( number should be provided by the users)
      Python
      •0•0•0•0•Updated Apr 16, 2024Apr 16, 2024

    • geneseekrcsv_parsing

      Public
      This script takes geneseekr output csv file as input to parse the stx1 and stx2 genes in the user specified output file
      Python
      •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • dorado_basecalling_demultiplexing

      Public
      This program is run on the GPU machine, where tools such as pod5 and dorado is installed
      Shell
      •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • source_and_resistance_categorizer

      Public
      Categorizes and assigns (1) isolation source and (2) antimicrobial classes isolates are resistant to using metadata files from NCBI Pathogen Finder datasets
      Python
      •0•0•0•0•Updated Sep 27, 2023Sep 27, 2023

    • ConFindr-GUI

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 28, 2023Aug 28, 2023

    • dorado_basecalling

      Public
      This bash script does the basecalling using dorado. you need to provide the path of the minknow fast5 directory and it does the magic
      Shell
      •0•0•0•0•Updated Aug 15, 2023Aug 15, 2023

    • MiseqHashR-GUI

      Public
      Contains the GUI application for the MiseqHashR app
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 30, 2023Jun 30, 2023

    • MiSeqHashR

      Public
      Create and store MD5 hashes of Illumina .fastq.gz files from sequencing runs
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 22, 2023Jun 22, 2023

    • python-script-to-mash-sketches

      Public
      This program calculates the mash sketches from the BestAssemblies direcory using all .fasta files
      Python
      •0•0•0•0•Updated Apr 4, 2023Apr 4, 2023

    • in_silico_PCR

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Oct 7, 2022Oct 7, 2022

    • FetaGenome2

      Public
      Creation of mock metagenomic datasets
      Python
      •
      MIT License
      •0•0•0•1•Updated Jun 21, 2022Jun 21, 2022

    • AMR_Summary

      Public
      AMR Summary combines the outputs from ResFinder and MOB-recon to report on plasmid-borne AMR genes
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 27, 2022Apr 27, 2022

    • sipprverse

      Public
      Python
      •
      MIT License
      •3•0•0•0•Updated Apr 21, 2022Apr 21, 2022

    • GeneSeekr

      Public
      Quick parallel BLAST for gene finding
      Python
      •
      MIT License
      •1•2•0•0•Updated Apr 13, 2022Apr 13, 2022

    • SigSeekr

      Public
      Python
      •
      MIT License
      •2•0•0•0•Updated Sep 4, 2020Sep 4, 2020

    • ParaTyper

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 17, 2020Feb 17, 2020

    • OLC_NAS_Tools

      Public
      Internal OLC program to retrieve sequence data from the local FreeNAS
      Python
      •2•1•0•0•Updated Jul 11, 2019Jul 11, 2019