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3genomesnp_pipeline

A pipeline to seperate NGS sequencing data into chloroplast, mitochondria and nuclear genomes, and then call SNPs in the 3 genomes respectively.

alphafold

Open source code for AlphaFold.

amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

an-association-between-gut-microbiome-and-obesity

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

bactopia

A flexible pipeline for complete analysis of bacterial genomes

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

bmgap

The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples

cecret

Nextflow workflow for our analysis of SARS-COV-2

csvtk

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

docker-builds

:package: :whale: Dockerfiles and documentation on tools for public health bioinformatics

enzyme_cutting_simulation_scripts

These scripts are used for silic simulation analysis of enzyme-cutting-genome

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

fastani

Fast Whole-Genome Similarity (ANI) Estimation

freyja

Depth-weighted De-Mixing

gdmets

gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

krakentools

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

longqc

LongQC is a tool for the data quality control of the PacBio and ONT long reads.

microbetrace

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

multi-ploidsnps

a GBS-based pipeline for calling SNPs from a group of samples with different ploidy.

mutagan

mycosnp-nf

only CDCgov/mycosnp-nf-1.4 works in HPG

nchhstp-dtbe-varpipe-wgs

This repository contains an analysis pipeline developed to characterize WGS output

npgeno

bioinformatics pipeline that could generate genome-wide SNP genotype data for a conventional genetic diversity analysis of a non-model plant species

orthophy

pasnpg

a GBS-based pipeline called paSNPg for protein-associated SNP (paSNP) discovery and genotyping in non-model organisms

pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

pfaster

pneumococcal FASTA serotype calling