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bifrost_dashboard

bifrost_enterobase

bifrost_min_read_check

Bifrost Component: Min Read Check - Checks that provided read files have a minimum number of reads for analysis

bifrost_run_launcher

bifrost_salmonella_subspecies_dtartrate

bifrost_seqsero

Component for running seqsero in Bifrost

bifrost_ssi_stamper

Bifrost Component: SSI Stamper - Runs SSI's QC check on samples using metrics generated from Assemblatron, Min Read Check and Whats my species

bifrost_test_data

bifrost_whats_my_species

Bifrost Component: Whats My Species - Checks species of sample and whether it's correct or not against a kraken DB

bio_api

REST API for triggering bioinformatic calculations from SOFI

bps_fbi_fsc_virulencefinder

Bash scripts to run virulencefinder and serotypefinder in local settings on ecoli fasta and fastq.gz files.

bps_fbi_scripts_clostyper

Tool to find mge (phages, plasmids, and transposons) in cdiff. Scripts that allow Clostyper to be run in slurm.

bps_fbi_sp_ecoli

Ecoli species specific scripts in nbdev2 format.

calc-script-demux_illumina

calc-script-find_run_diff

cc398_global_phylogeny

Preliminary work of CC398 global phylogeny

cd-mrg-bruker

Scripts and documentation for Bruker software

cd-mrg-fakedata

Notebook showing how to create fake data for our typical case-control studies.

cd-mrg-metabolomics_autism

cd-mrg-metabolomics_summerschool_2023

This repository contains teaching material for the 3rd International Summer School on Non-Targeted Metabolomics Data Mining for Biomedical Research

cd-mrg-plateplanner

Python package to create multi-well plate layouts for specimen sample data. Automatically distributes quality control samples according to scheme in config file.

cge_pointfinder_kma

Run CGE pointfinder in kma mode

cgmlstsearch

Proof of concept implementation for indexed similarity search of a cgMLST profile against a database.

chewie_datadumper

Simple prototype script for integration of chewieSnake in Bifrost.

cleanrecomb

Cleans putative recombination events from a SNP matrix

covid_variant_calling

dash-scroll-up

Dash component to add custom button to scroll to the top of the page.

diseasy

diseasystore

R package that provides a feature store tailored towards disease modelling

ecoli_pathotypes