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phytools

piml-toolbox

PiML (Python Interpretable Machine Learning) toolbox for model development and validation.

pirate

A toolbox for pangenome analysis and threshold evaluation.

plottree

poppunk

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

post_fastgear

Post fastGEAR plotting script

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

prophet

pyani

Python module for average nucleotide identity analyses

pyseer

SEER, reimplemented in python 🐍🔮

qiime2

Official repository for the QIIME 2 framework.

rapt-ncbi

Read Assembly and Annotation Pipeline Tool

recovery_determinants_study

Data and scripts of Antibiotic Recovery Study

reformat

Scripts for reformatting data. Mainly from tab separated to an esoteric program specific format

rmap

Bacterial analysis Toolbox for profiling the Resistome of ESKAPE pathogens using WGS

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

samtools

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

sarscov2lineages

sarscov2phylo

Global phylogenies of SARS-CoV-2 sequences

seq-scripts

scripts for sequence and feature conversion, annotation, analysis ...

seqsero

Salmonella serotyping from genome sequencing data

seqtk

Toolkit for processing sequences in FASTA/Q formats

sistr_cmd

SISTR (Salmonella In Silico Typing Resource) command-line tool

snippy

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

snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

split_multi_fasta

Split multi fasta file into single fasta files

variant_definitions

vcf_parser

Simple vcf parser, based on PyVCF

vcfparser

Parse iVar output into beautiful heatmaps based on pre-defined list of SNVs associated with COVID-19 VOC/VOIs