emilyncosta
As a Biologist with a PhD in Microbiology, I'm fascinated by Mycobacteria. My research focuses on Molecular Epidemiology using WGS and bioinformatics tools. =)
Stellenbosch UniversityCape Town, South Africa
Pinned Repositories
Academic-CV
CPqGMFiocruzBA_MTB_MDR-XDR_nf
ECCS_website
My Blog and CV
IEC-PA_Figures_PhDEmilyn
Isolates images from PDF for publication in journals.
LABBACT-INI-FIOCRUZRJ_Mtb_MonoINH_nf
LABMAM-FIOCRUZRJ_Legionella_nf
LABMAM-FIOCRUZRJ_Mbovishuman_nf
UFRJ_Public_PhDEmilyn
Für Emilyn
UNIFESP_NTM_newspecies-nf
Paper "Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo Zoological Park Foundation in Brazil"
USP-RP_Mtb_prison_SP_nf
Tb-Profiler analysis in AWS Batch
emilyncosta's Repositories
emilyncosta/UNIFESP_NTM_newspecies-nf
Paper "Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo Zoological Park Foundation in Brazil"
emilyncosta/Academic-CV
emilyncosta/IEC-PA_Figures_PhDEmilyn
Isolates images from PDF for publication in journals.
emilyncosta/UFRJ_Public_PhDEmilyn
Für Emilyn
emilyncosta/USP-RP_Mtb_prison_SP_nf
Tb-Profiler analysis in AWS Batch
emilyncosta/CPqGMFiocruzBA_MTB_MDR-XDR_nf
emilyncosta/ECCS_website
My Blog and CV
emilyncosta/IEC-PA_Mtb-L1_phylogeny_PhDEmilyn_nf
emilyncosta/LABBACT-INI-FIOCRUZRJ_Mtb_MonoINH_nf
emilyncosta/LABMAM-FIOCRUZRJ_Legionella_nf
emilyncosta/LABMAM-FIOCRUZRJ_Mbovishuman_nf
emilyncosta/CRISPRbuilder-TB
Reconstruct M.tuberculosis CRISPR locus from WGS data
emilyncosta/cryptic-ecoffs
Data and code to reproduce the figures and tables in the CRyPTIC ECOFF/ECV paper
emilyncosta/DeeplexiconDemuxAndSplit
Wrapper pipeline script running demux and split on nanopore fast5 and fastq data using the Deeplexicon pipeline
emilyncosta/ENA-download-and-spotyping
emilyncosta/LABMAM-FIOCRUZRJ_Mbovis_BCG_nf
emilyncosta/LABMAM-FiocruzRJ_Mbovis_MScLuiz_nf
emilyncosta/LABMAM-FIOCRUZRJ_Mtb_Eldholm
Eldholm genomes
emilyncosta/lineage_1_malawi_nf
emilyncosta/MTBseq_source
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
emilyncosta/mtc
Python package to annotate WGS genomes of tuberculosis and get information about their CRISPR
emilyncosta/NCBI_submission_upload_genomes_via_ftp
emilyncosta/snippy
emilyncosta/tbvcfreport
Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s)
emilyncosta/transflow
A snakemake workflow for WGS-based tuberculosis transmission analysis
emilyncosta/TransPhylo
Reconstruction of transmission trees using genomic data
emilyncosta/USP-RP_rdanalyzer_PhDEva
emilyncosta/wgs_lineage_1_resistance