R implementation of the LEfSe method

usearCh basEd ampliCon pIpeLine for Illumina dAta

Studying the statistical relationship between species and groups of sites

A grammar of graphics for comparative genomics

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

Growthcurver is an R package that fits growth curve data to a standard form of the logistic equation common in ecology and evolution whose parameters (the growth rate, the initial population size, …

Code to create a PRG from a Multiple Sequence Alignment file

SEER, reimplemented in python 🐍🔮

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

hybrid assembly pipeline for bacterial genomes

A tool to circularize genome assemblies

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

Pilon is an automated genome assembly improvement and variant detection tool

A versatile pairwise aligner for genomic and spliced nucleotide sequences

viralFlye pipeline

viralVerify: viral contig verification tool

Phylogenetic orthology inference for comparative genomics

⚡ ♒ Rapid prokaryotic genome annotation

Pipelines 2022

The seqtime R package provides functions to analyse sequencing data time series and to simulate community dynamics

An R package for microbial community analysis in an environmental context

MIcrobial Network Analysis

Prodigal Gene Prediction Software

Create statistic summary of an Oxford Nanopore read dataset

The is mostly a wrapper tool using phyloseq and microbiome R packages.

Maximum Likelihood Amplicon Pipeline