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16s_np

anammxox_pathway_evo_publ

bioconda-recipes

Conda recipes for the bioconda channel.

bioinfo_scripts

A mix of scripts.

cansnper

A hierarchical genotype classifier of clonal pathogens

emg-toolkit

MGnify API toolkit

figtree_scripts

Collection of scripts for preparing tree-files for FigTree

genomes_from_taxa

Download genome data from NCBI using taxonomic id

jsonapi-client-feedstock

A conda-smithy repository for jsonapi-client.

linminup

Linux code distribution for minUP

ls-bsr

Large scale Blast Score Ratio (BSR) analysis

nanosim

Nanopore sequence read simulator

np-kraken-win

Run kraken in Docker using locally basecalled sequences from MinION.

orthofinder

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

phylogenetic_tree_reconstruction

poretools

a toolkit for working with Oxford nanopore data

programming_lecture

Jupyter Notebook for Introduction to Programming, Bioinformatic Analyses 1

pylogeny

A tool for conversion from assorted NCBI Accessions to NCBI Taxonomy IDs

ruscripts

Scripts for implementing read until and other examples.

schavott

Assembly and scaffolding of bacterial genomes in real time using MinION-sequencing

spoon-knife

This repo is for demonstration purposes only.

tada

A Snakemake-workflow to sample taxa from sequence databases based on taxonomical or phylogenetic information

treemmer

Python tool to reduce size and redundancy of phylogenetic datasets

uabimicrobium_paper

wgfast

Whole genome focused array SNP typer