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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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This is the user guide for the Shark CentOS-8 Slurm-20.02 cluster. This will give the user a short introduction to the cluster and how to use it.
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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 / hutspot
GNU Affero General Public License v3.0Snakemake-based WES/IDP pipeline for LDGA.
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Sam Nooij / Automated bacterial assembly from PacBio HiFi
BSD 3-Clause "New" or "Revised" LicenseAutomated and parallelised workflow to assemble PacBio HiFi reads of bacteria whole-genome sequencing. Also subsamples reads before assembly and re-orients resulting contigs to the 'correct' starting position.
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Mirrors / backtranslate
MIT LicenseUpdated -
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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A collection of semi-reusable scripts, which are not part of any official toolchain
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De Coster / APqr Final
GNU General Public License v3.0 or laterUpdated -
Mirrors / mutalyzer
Creative Commons Attribution Share Alike 4.0 InternationalMirror of https://github.com/LUMC/mutalyzer.git
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