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Top 10 infectious-diseases open source projects

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

✭ 27

python shell TeX Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Predict plasmids from uncorrected long read data

✭ 27

python TeX Dockerfile bioinformatics research nanopore genomics pathogen bioinformatics-pipeline pacbio global-health kmer oxford-nanopore plasmid infectious-diseases long-reads uncorrected plasmidfinder

Assembling the cause of phenotypes and genotypes from NGS data

✭ 27

python shell Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

R Package for individual based epidemiological models

✭ 20

r C++TeX rstats agent-based-modeling epidemiology r-package infectious-diseases individual-based-modelling

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

✭ 17

python TeX shell Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Multilocus sequence typing by blast using the schemes from PubMLST

✭ 22

perl shell bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

assembly improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

✭ 46

perl bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Domain-Specific Modeling for Epidemiology

✭ 43

smalltalk pharo epidemiology mathematical-modelling pharo-smalltalk model-driven-engineering infectious-diseases

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

✭ 103

python c M4 shell Makefile r bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Finds SNP sites from a multi-FASTA alignment file

✭ 182

c M4 perl C++bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

1-10 of 10 infectious-diseases projects