insapathogenomics
Bioinformatics Unit of the Portuguese National Institute of Health Dr. Ricardo Jorge (INSA),
INSALisbon
Pinned Repositories
algn2pheno
A bioinformatics tool for rapid screening of genetic features (nt or aa changes) potentially linked to specific phenotypes
ComparingPartitions
Colection of python functions for Partition Comparison - See www.comparingpartitions.info for more information
countDNABox
Count the occurrence and distance of two DNA sequences in multi-fasta/fastq files
fastq-handler
A python module to process ONT fastq files by concatenating reads as they are generated during a sequencing run
getCoverage
GrapeTree
GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html
mutation_profile
Identify the sequence context flanking SNPs of interest and screen for potential profiles/signatures of interest
ReporTree
A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
ReporType
Flexible bioinformatics tool for targeted loci screening and typing
WGS_cluster_congruence
This repository contains the scripts used for the cluster congruence analysis of multiple bioinformatics pipelines and species.
insapathogenomics's Repositories
insapathogenomics/ReporTree
A surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data
insapathogenomics/mutation_profile
Identify the sequence context flanking SNPs of interest and screen for potential profiles/signatures of interest
insapathogenomics/ReporType
Flexible bioinformatics tool for targeted loci screening and typing
insapathogenomics/algn2pheno
A bioinformatics tool for rapid screening of genetic features (nt or aa changes) potentially linked to specific phenotypes
insapathogenomics/cml_efsa.wgs.onehealth_facilitator
A surveillance-oriented script to facilitate the deployment of the EFSA's Whole Genome Sequencing OneHealth analytical pipeline
insapathogenomics/WGS_cluster_congruence
This repository contains the scripts used for the cluster congruence analysis of multiple bioinformatics pipelines and species.
insapathogenomics/ComparingPartitions
Colection of python functions for Partition Comparison - See www.comparingpartitions.info for more information
insapathogenomics/countDNABox
Count the occurrence and distance of two DNA sequences in multi-fasta/fastq files
insapathogenomics/fastq-handler
A python module to process ONT fastq files by concatenating reads as they are generated during a sequencing run
insapathogenomics/getCoverage
insapathogenomics/GrapeTree
GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html
insapathogenomics/insaflu_docs
INSaFLU [https://insaflu.insa.pt] DOCUMENTATION
insapathogenomics/TreeCluster
Efficient phylogenetic clustering of viral sequences
insapathogenomics/vcf2mst
Hamming Distance based Minimum Spanning Tree from Samples vcf using graptree