TipToft
TipToft: detecting plasmids contained in uncorrected long read sequencing data - Published in JOSS (2019)
Multilocus sequence typing by blast from de novo assemblies against PubMLST
Multilocus sequence typing by blast from de novo assemblies against PubMLST - Published in JOSS (2016)
SaffronTree
SaffronTree: Fast, reference-free pseudo-phylogenomic trees from reads or contigs. - Published in JOSS (2017)
GFF3toEMBL
GFF3toEMBL: Preparing annotated assemblies for submission to EMBL - Published in JOSS (2016)
taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
https://github.com/ccdmb/catastrophy
CATAStrophy predicts filamentous plant pathogen lifestyle characteristics based on their CAZyme composition.
https://github.com/cidgoh/grdi_amr_one_health
A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
https://github.com/cidgoh/cancogen_contextual_data_specification
A data specification for harmonizing One Health Canadian COVID pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a the DataHarmonizer, supported by field and reference guides as well as different curation and new term request SOPs.
amr
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
nf-uno
metagenomics pipeline supporting The UnO Project for identifying pathogens in common across outbreak samples