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Sam Nooij / metagenomics-scaffold-classification
BSD 2-Clause "Simplified" LicenseAn automated workflow for taxonomically classifying assembled scaffolds from metagenomics data.
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Sam Nooij / cookiecutter-data-science
BSD 2-Clause "Simplified" LicenseUpdated -
Sam Nooij / metagenomics-plasmid-assembly
BSD 2-Clause "Simplified" LicenseAn automated workflow for generating metagenomic assemblies with a focus on reconstructing plasmids.
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Sam Nooij / Jovian screener
GNU General Public License v3.0 onlyA pipeline to automatically screen the output by Jovian for the presence of species and sequences (genes) of interest, and quantify them.
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hem / hamlet
MIT LicenseRNA-seq pipeline for AML diagnostics. Illustration from Anatomy & Physiology, licenced under the Creative Commons Attribution 3.0 Unported
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Pipeline to pre-process vcf and gvcf files and submit them to varda.lumc.nl
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Sam Nooij / rCDI resistome and MDRO analyses
BSD 3-Clause "New" or "Revised" LicenseAnalyses of antimicrobial resistance genes in metagenomic data from patients with (multiple) recurrent Clostridioides difficile infections and their faecal microbiota transplantation donors - with culture data from multidrug resistant organisms
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Klinische Genetica / capture-lumc / vtools
MIT LicenseVarious tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed
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Hoogenboom / fdstools
BSD 3-Clause "New" or "Revised" LicenseData analysis tools for Next Generation Sequencing of forensic DNA markers, including tools for characterisation and filtering of PCR stutter artefacts and other systemic noise, and for automatic detection of the alleles in a sample.
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extractor / gesa
MIT LicenseLibrary implementing Generalized Enhanched Suffix Arrays (GESAs)
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Engraftment calculations based on One Codex species-level taxonomic classifications of shotgun metagenomic read sets of the FECBUD trial - a collaboration between the Netherlands Donor Feces Bank and Vedanta Biosciences.
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Sam Nooij / pks in rCDI metagenomes analysis
BSD 2-Clause "Simplified" LicenseAnalysis scripts used to analyse the procarcinogenic pks gene island in metagenomes of multiple recurrent Clostridioides difficile infected patients and their corresponding healthy donors from the Netherlands Donor Feces Bank.
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