Pathogen Informatics, Wellcome Sanger Institute

All

92 repositories

Unicycler
Public
hybrid assembly pipeline for bacterial genomes
C++
•
GNU General Public License v3.0
•135•0•0•1•Updated Dec 4, 2024Dec 4, 2024
assorted-sub-workflows
Public
Nextflow
•
GNU Affero General Public License v3.0
•0•0•0•0•Updated Dec 3, 2024Dec 3, 2024
nextflow-commons
Public
Store of generic templates and scripts for nextflow pipelines
Nextflow
•
GNU Affero General Public License v3.0
•0•1•0•2•Updated Nov 28, 2024Nov 28, 2024
generate_mags
Public
Nextflow
•0•1•0•0•Updated Nov 27, 2024Nov 27, 2024
long-read-ampliseq
Public
Nextflow
•
GNU Affero General Public License v3.0
•0•2•0•0•Updated Nov 19, 2024Nov 19, 2024
Fastaq
Public
Python3 scripts to manipulate FASTA and FASTQ files
bioinformatics research genomics pathogen sequencing next-generation-sequencing global-health infectious-diseases
Python
•
Other
•21•70•8•2•Updated Nov 12, 2024Nov 12, 2024
pymummer
Public
Python3 module for running MUMmer and reading the output
Python
•
Other
•11•30•3•0•Updated Nov 12, 2024Nov 12, 2024
bentley-app
Public
Static site for Stephen Bentley's group
JavaScript
•0•0•0•1•Updated Nov 6, 2024Nov 6, 2024
Multiple-mappings-to-bam
Public
A GSoC project - Nextflow pipeline updating the legacy Python2 Multiple mappings to bam to nextflow.
Python
•0•2•0•0•Updated Aug 23, 2024Aug 23, 2024
nano-rave
Public
Nextflow pipeline designed for rapid onsite QC and variant calling of Oxford Nanopore data (following basecalling and demultiplexing with Guppy).
Nextflow
•
GNU Affero General Public License v3.0
•4•11•1•0•Updated Aug 9, 2024Aug 9, 2024
TpRNAseq
Public
A bacterial RNAseq pipeline, designed for analysis of Treponema pallidum data
Nextflow
•
MIT License
•0•0•0•0•Updated Aug 8, 2024Aug 8, 2024
nextflowtool
Public
Groovy
•
GNU Affero General Public License v3.0
•0•0•0•0•Updated Jul 22, 2024Jul 22, 2024
sh16_scripts
Public archive
Deprecated scripts for reference only
Python
•0•0•0•0•Updated Jul 18, 2024Jul 18, 2024
software-tracker
Public
API and helper scripts for the pathogen software installation tracking database
Python
•
MIT License
•1•0•1•0•Updated Jul 12, 2024Jul 12, 2024
Artemis
Public
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
bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases
Java
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Other
•77•239•29•4•Updated Jun 15, 2024Jun 15, 2024
Phylign
Public
Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on a laptop within a few hours.
Python
•
Other
•7•0•0•0•Updated May 22, 2024May 22, 2024
BaGPipe
Public
A bacterial GWAS pipeline written in Nextflow that uses Pyseer; Part III Project for Systems Biology at the University of Cambridge
Nextflow
•
MIT License
•1•2•0•0•Updated May 2, 2024May 2, 2024
circlator
Public
A tool to circularize genome assemblies
bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases
Python
•
Other
•60•233•56•5•Updated Apr 6, 2024Apr 6, 2024
python_fun
Public
Python
•
Other
•1•1•0•0•Updated Mar 13, 2024Mar 13, 2024
bactgen-training-app
Public
Static site for training on the Juno/GPS2 projects
HTML
•1•0•0•0•Updated Feb 29, 2024Feb 29, 2024
paminfo-open-lab-event
Public
CSS
•0•1•0•0•Updated Feb 8, 2024Feb 8, 2024
paminfo-training-FE
Public
A lightweight frontend application used for testing applicants
CSS
•1•0•0•0•Updated Jan 26, 2024Jan 26, 2024
ariba
Public
Antimicrobial Resistance Identification By Assembly
bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases
Python
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Other
•55•172•44•4•Updated Oct 12, 2023Oct 12, 2023
external-import
Public
Import external data into our tracking databases
Python
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Other
•1•0•0•0•Updated Aug 16, 2023Aug 16, 2023
Bio-Tradis
Public
A set of tools to analyse the output from TraDIS analyses
bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases
Perl
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Other
•29•23•17•0•Updated Aug 8, 2023Aug 8, 2023
seroba
Public
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases
Python
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Other
•18•19•22•2•Updated Jul 13, 2023Jul 13, 2023
assembly-stats
Public
Get assembly statistics from FASTA and FASTQ files
bioinformatics research genomics pathogen sequencing next-generation-sequencing global-health infectious-diseases
C++
•
Other
•23•115•3•0•Updated May 9, 2023May 9, 2023
multimapper
Public
Updated conversions of Simon Harris' pipelines
Python
•0•0•0•0•Updated Mar 23, 2023Mar 23, 2023
Bio-AutomatedAnnotation
Public
Perl module to take in an genomic assembly and produce annoation
Perl
•
Other
•8•1•0•0•Updated Mar 14, 2023Mar 14, 2023
monocle
Public
Python
•
Other
•0•1•0•0•Updated Mar 9, 2023Mar 9, 2023