GENPAT (Italian National Reference Centre for WGS of microbial pathogens)
- 13 followers
- Teramo, Abruzzo, Italy
- https://genpat.izs.it/
- genomica@izs.it
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cgmlst-dists-py
cgmlst-dists-py PublicHigh-performance pairwise Hamming distance calculator for cgMLST data with GPU acceleration
Repositories
- mm2-geo Public
Geometry-guided band-doubling for the minimap2 gap-filling DP (faster at identical variant-calling F1; composes with mm2-fast)
- chewcall Public
Fast cgMLST/wgMLST allele caller with SIMD Smith-Waterman scoring (parasail) and an offline schema-side minimizer-overlap audit. 10.7–22.3× faster than chewBBACA with 100% DNA-sequence agreement on bilaterally callable cells.
- phenocal Public
Genome-anchored calibration of a continuous phenotype across cohorts, with uncertainty-propagated probabilistic labels
- mm2-geo-reproducibility Public
Superseded: first-submission material of mm2-geo; current version on branch 'reproducibility' of genpat-it/mm2-geo
- cgDist Public
Ultra-fast SNP/indel-level distance calculator for core and whole genome MLST (cg/wgMLST) analysis in bacterial genomics
- bioinformatics-platform-comparison Public
Documented, correctable comparison of bacterial and viral genomic-surveillance platforms: every value backed by a cited source and a verbatim passage. Corrections via pull request.
- cohesive-llm Public
Self-hostable AI platform that generates Nextflow DSL2 pipelines for the cohesive-ngsmanager framework
- cohesive-jenkins Public
- cohesive-ngsmanager Public
- cohesive Public
Docker-based COHESIVE Information System (CIS) for One Health surveillance, outbreak investigation, and risk assessment of zoonoses.
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