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big-list-of-naughty-strings

The Big List of Naughty Strings is a list of strings which have a high probability of causing issues when used as user-input data.

clean_mlst_results

Simple script for cleaning and collating MLST result files

colltyper

Typing of TB using Coll-2015 scheme

datasets

A collection of public datasets

dist-outliers

Detection of outliers in distance matrices

emm_typing

Typing of emm genes in Streptococcus pyogenes

ffiscripts

A collection of scripts used during my time at FFI

fhiscripts

filter-plasmid-contigs-bacillus

A script for filtering contigs by header name

globall4scripts

A collection of scripts used for the global L4 MTB phylogeography paper

lombardy-norway

Data about flights between Norway and Lombardy, and nCoV-19 cases

niph_tb_pipeline

WGS pipeline for Mycobacterium tuberculosis at the Norwegian Institute of Public Health (NIPH)

originator

Rotate circular replicon to start with dnaA gene

pooledsampling-covid-simulation

Estimating the effect of pooled sampling in testing for Covid-19 through simulations in R

puppetmaster

Tools for manipulating sequencing data, multiple sequence alignments and phylogenetic trees

scoary

Pan-genome wide association studies

simulate_pan_genome

Simulates a pan-genome

snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

stx_subtyping

tartrate

Script to differentiate typhoid and non-typhoid Salmonella by analysis of the STM3356 ORF

tb

Nextstrain build for tuberculosis

tb-moldova

tb-moldova-203

tb-moldova-203-alt

tb-moldova-full