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This was the temporary repository in which the published version of PAROS was created and this repository was temporarily made visible during the peer review process.
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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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Sam Nooij / R. gnavus MAGs from rCDI patients
BSD 3-Clause "New" or "Revised" LicenseGenerate metagenome-assembled genomes of Ruminococcus gnavus from recurrent Clostridioides difficile infected patient metagenomes
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Sam Nooij / Create MAGs from filtered reads-Kraken
BSD 3-Clause "New" or "Revised" LicenseUse Kraken2 to quickly classify metagenomic reads and extract reads of taxa of interest to then assemble metagenomic assembled genomes (MAGs)
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Sam Nooij / FECBUD functional analysis-HUMAnN
BSD 3-Clause "New" or "Revised" LicenseFunctional metagenomics analysis using the HUMAnN tool version 3
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Sam Nooij / metagenomics-bacterial-profiling
GNU General Public License v3.0 or laterTaxonomic profiling of metagenomics reads using bacterial and Archaeal marker genes
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Sam Nooij / screen_pks_in_polyposis_fecal_metagenomes
BSD 2-Clause "Simplified" LicenseScreen fecal metagenomes of polyposis patients for the presence of the pks gene island of procarcinogenic E. coli
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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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Mutalyzer / mutalyzer2
Creative Commons Attribution Share Alike 4.0 InternationalHGVS variant nomenclature checker
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Chouaref / Snakemake_ChIP_seq_pipeline
MIT LicenseRepository containing a Snakemake ChIPseq pipeline for SE and PE datasets
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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 / metagenomics-preprocessing
BSD 2-Clause "Simplified" LicenseA Snakemake workflow to automatically handle metagenomics preprocessing (i.e. host removal and low-quality trimming).
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