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pathogen-informatics-training

pgsc_calc

The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation

phandango

an interactive viewer for populations of bacterial genomes linked by a phylogeny

plant-scripts

Scripting analyses of genomes in Ensembl Plants

plotly.r

An interactive graphing library for R

powershell

PowerShell for every system!

primer3tools

Design PCR primers and check uniqueness across multiple genomes

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

py4bio

Public data for the book Python for Bioinformatics

pyseer

SEER, reimplemented in python 🐍🔮

python-basics-exercises

Python Basics: A Practical Introduction to Python 3

r-for-data-analysis

Everyone is a data analyst. The purpose of this book is to inspire and enable anyone who reads it to reconsider the methods they currently employ to analyse data.

readfq

Fast multi-line FASTA/Q reader in several programming languages

readfq.v8_meta

roary

Rapid large-scale prokaryote pan genome analysis

samtools

Tools (written in C using htslib) for manipulating next-generation sequencing data

scoary

Pan-genome wide association studies

seaborn

Statistical data visualization in Python

seaborn-data

Data repository for seaborn examples

seer

sequence element (kmer) enrichment analysis

seqsero2

SeqSero2

seqtk

Toolkit for processing sequences in FASTA/Q formats

seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

sickle

Windowed Adaptive Trimming for fastq files using quality

sllobs-biostats

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

snp_finder

snp_pipeline

Pipeline for reference-based variant (SNP/indels) calling from raw data to phylogeny.

snpfilt

A package to identify SNPs using reference-free assembly