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Starred repositories
AlleleFinder is a tool for identifying allele genes from polyploid genome.
A Python library for manipulation of CIGAR, MSA, and other alignment formats.
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
MAGinator - Accurate SNV calling and profiling of MAGs
A repository of R usage tips for data cleaning, data mining, data visualisation, statistical inference and machine learning
Structural Variant Identification Method using Genome Assemblies
Multiplatform plotting library based on the Grammar of Graphics
geNomad: Identification of mobile genetic elements
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
snipit: summarise snps relative to your reference sequence
Efficient phylogenetic tree inference for massive taxonomic datasets
Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.
Python package to plot a phylogenetic tree on an existing matplotlib axis.
Make awesome display tables using Python.
PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.
Tool to visualise and cluster assembly contigs using kmers
A matplotlib-based library to produce sankey plots
Shiny app intended to analyze flow cytometry data to produce fluorescence histograms
Hybrid error correction of long reads using colored de Bruijn graphs
Make sankey, alluvial and sankey bump plots in ggplot
