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automate_ksnp

bash_one-liners

Bash one-liners useful for bioinformatics

bioawk

BWK awk modified for biological data

bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

biomic2starlims

Converts BIOMIC MIC and zone diameter data to the Starlims format.

c-sstar

CLI Sequence Search Tool for Antimicrobial Resistance

compare_gene_databases

Scripts for generating and comparing gene databases with each other

core-genome-size-estimation

Estimate the core genome size for a group of isolates

dada2_workflow

A simple workflow for processing 16s sequence data with DADA2

data_storage

Research output storage

determine-codon-usage

Determines the codon usage for each amino acid for a single sequence

genomics_workflow

Bacterial assembly and annotation pipeline

glimmer-scripts

Small utility scripts for GLIMMER output

groot

A resistome profiler for Graphing Resistance Out Of meTagenomes

hmmer-scripts-

Scripts that deal with HMMer output

interproscan-scripts

Utility scripts for interproscan output

krakentools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

metagenomics_workflows

Repository for storing metagenomics workflows

ml_tutorials

phylogenetics_scripts

Scripts for handling WGS SNP data

picrust2

Code, unit tests, and tutorials for running PICRUSt2

placnet2fasta

Converts PLACNET output to a FASTA file containing plasmid contigs

pull_genes_from_prokka_output

Pull genes of interest from Prokka genome annotation output

quaisar-h

Pipeline designed to analyze short reads for Quality, Assembly, Identification, Sequence_typing, Annottation, and Resistance_mechanisms for Hospital acquired bacterial infections

quaisar_singularity

Containerized version of QuAISAR

sam-file-scripts

Scripts for handling SAM files

seq2hla_workflow

Pipeline for HLA typing from RNA-Seq data

sequence-scripts

Random utility scripts for genomics data

sequence-search-tool-for-antimicrobial-resistance-sstar-

Antimicrobial resistance gene predictor

small_shell-scripts

Tiny shell scripts for various tasks