Senior Scientist at Clinical Microbiomics A/S
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Language: Python
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Using the jedi autocompletion library for VIM.
Scripts to download genomes from the NCBI FTP servers
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
Variational autoencoder for metagenomic binning
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
CarveMe: genome-scale metabolic model reconstruction
Virus Identification By iteRative ANnoTation
De novo Extraction of Strains from MetAgeNomes
SMETANA: a tool to analyse interactions in microbial communities