judithbergada
PhD Student, currently investigating bacterial infections. MSc in Bioinformatics and Computational Biology.
ETH Zürich & University of ZürichSwitzerland
Pinned Repositories
judithalberto.wedding
Wedding webpage.
BaColonyzer
BaColonyzer is a software to quantify the fitness of bacterial cultures growing on solid agar, based on time-course pictures
BaQFA-R-Package
BaQFA is an R package used to import BaColonyzer generated data and to fit growth models to these data. Other data can also be imported if in correct format.
bacolonyzer
BaColonyzer is a software to quantify the fitness of bacterial cultures growing on solid agar, based on time-course pictures
CASPR
CASPR pipeline.
Pipeline_GenomeAnalysis
Pipeline to assemble paired-end sequencing reads, annotate the resulting contigs, compare the genome content across sequences and determine the variants (SNPs).
Pipeline_HybridAssemblies
Pipeline to create hybrid assemblies from long and short reads, annotate the genomes, compare the genome content across strains, determine the variants (SNPs), and identify the differentially located insertion sequences (DLIS).
Pipeline_MLST
Pipeline to assemble paired-end sequencing reads and scan resulting contig files against PubMLST typing schemes
Pipeline_RNAseq
Pipeline to perform end-to-end RNAseq analyses
webpage-demo
Tutorial to create documentation webpages. You can see the result in this webpage:
judithbergada's Repositories
judithbergada/bacolonyzer
BaColonyzer is a software to quantify the fitness of bacterial cultures growing on solid agar, based on time-course pictures
judithbergada/CASPR
CASPR pipeline.
judithbergada/Pipeline_GenomeAnalysis
Pipeline to assemble paired-end sequencing reads, annotate the resulting contigs, compare the genome content across sequences and determine the variants (SNPs).
judithbergada/Pipeline_HybridAssemblies
Pipeline to create hybrid assemblies from long and short reads, annotate the genomes, compare the genome content across strains, determine the variants (SNPs), and identify the differentially located insertion sequences (DLIS).
judithbergada/Pipeline_MLST
Pipeline to assemble paired-end sequencing reads and scan resulting contig files against PubMLST typing schemes
judithbergada/Pipeline_RNAseq
Pipeline to perform end-to-end RNAseq analyses
judithbergada/webpage-demo
Tutorial to create documentation webpages. You can see the result in this webpage: