emilhaegglund
Bioinformatics and data analytics, PhD in Molecular Evolution. Currently employed by Olink.
OlinkUppsala
Pinned Repositories
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
schavott
Assembly and scaffolding of bacterial genomes in real time using MinION-sequencing
TADA
A Snakemake-workflow to sample taxa from sequence databases based on taxonomical or phylogenetic information
uabimicrobium_paper
emilhaegglund's Repositories
emilhaegglund/TADA
A Snakemake-workflow to sample taxa from sequence databases based on taxonomical or phylogenetic information
emilhaegglund/schavott
Assembly and scaffolding of bacterial genomes in real time using MinION-sequencing
emilhaegglund/uabimicrobium_paper
emilhaegglund/anammxox_pathway_evo_publ
emilhaegglund/figtree_scripts
Collection of scripts for preparing tree-files for FigTree
emilhaegglund/16s_np
emilhaegglund/bioconda-recipes
Conda recipes for the bioconda channel.
emilhaegglund/bioinfo_scripts
A mix of scripts.
emilhaegglund/CanSNPer
A hierarchical genotype classifier of clonal pathogens
emilhaegglund/emg-toolkit
MGnify API toolkit
emilhaegglund/Genomes_from_taxa
Download genome data from NCBI using taxonomic id
emilhaegglund/jsonapi-client-feedstock
A conda-smithy repository for jsonapi-client.
emilhaegglund/linminUP
Linux code distribution for minUP
emilhaegglund/LS-BSR
Large scale Blast Score Ratio (BSR) analysis
emilhaegglund/NanoSim
Nanopore sequence read simulator
emilhaegglund/np-kraken-win
Run kraken in Docker using locally basecalled sequences from MinION.
emilhaegglund/OrthoFinder
Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"
emilhaegglund/phylogenetic_tree_reconstruction
emilhaegglund/poretools
a toolkit for working with Oxford nanopore data
emilhaegglund/programming_lecture
Jupyter Notebook for Introduction to Programming, Bioinformatic Analyses 1
emilhaegglund/PYlogeny
A tool for conversion from assorted NCBI Accessions to NCBI Taxonomy IDs
emilhaegglund/RUscripts
Scripts for implementing read until and other examples.
emilhaegglund/Spoon-Knife
This repo is for demonstration purposes only.
emilhaegglund/Treemmer
Python tool to reduce size and redundancy of phylogenetic datasets
emilhaegglund/wgfast
Whole genome focused array SNP typer