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augur

Pipeline components for real-time virus analysis

auspice

Web app for visualizing pathogen evolution

autm-rb

Another theme for Jekyll

baltic

baltic - backronymed adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. Development is back on the evogytis/baltic branch (i.e. here).

carp_browser

circos_pangenome

Calculates overlap of multiple genomes and prepares files for CIRCOS visualization software

core_genome_scripts

extractbyid

Extract sequences from file using subset of sequence IDs

fit_tools

tools for analysing garmin fit files

geel_crim

genome_tools

globalcoralmicrobiomes

Statistical and graphical analysis of coral microbiomes. For a detailed post explaining these, head to:

jev_assembly_pipe

Snakemake pipeline to assemble JEV genomes from primer tiling data

kmer_tools

Set of utilities for analysing kmer profiles in NGS

mappd

Metagenomic Analysis Pipeline for Pathogen Discovery

med-paper-figure-6

A bunch of embarrassing ad-hoc python scripts to generate the alluvial diagram

metagenomicbinner

Genome binner for host-associated bacteria

microbimeplots

Analysis of coral microbiome 16S data using R and phyloseq. A detailed post is available here:

microbiomemap

A detailed post on this analysis is available here:

miscpython

mothurtocytoscape

narratives

Narrative markdown files accessed via nextstrain.org/narratives/x

neavemj.github.io

nextstrain_builds

normalizing_rna-seq

seleniumcamp

seq_tools

useful python scripts for NGS data manipulation

sphinx-themes.org

https://sphinx-themes.org

symbin

tv_scraper