All Git Users → sanger-pathogens

14 open source projects by sanger-pathogens

Rapid large-scale prokaryote pan genome analysis

✭ 176

perl bioinformatics research genomics sequencing

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

✭ 135

java bioinformatics research genomics sequencing

3. Circlator

A tool to circularize genome assemblies

✭ 121

python bioinformatics research genomics sequencing

4. Ariba

Antimicrobial Resistance Identification By Assembly

✭ 96

python bioinformatics research genomics sequencing

5. Gubbins

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

✭ 67

c bioinformatics research genomics sequencing

6. gff3toembl

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

7. pymummer

Python3 module for running MUMmer and reading the output

✭ 22

python shell

8. plasmidtron

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

9. companion

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

✭ 21

lua groovy ruby Dockerfile shell perl Nextflow bioinformatics pipeline parasites annotation genomics genome

10. saffrontree

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

11. vr-codebase

The overall codebase developed and used by the Vertebrate Resequencing group at the Sanger Institute

✭ 12

12. mlst check

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

13. 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

14. snp-sites

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

1-14 of 14 user projects