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ILVO-Genomics / metabarcoding / MetaBarDB
MIT No AttributionUpdated -
This repository contains a Snakemake workflow tailored for assembling bacterial genomes from long-read data generated with R10.4.1 simplex reads from Oxford Nanopore Technologies and includes several QC steps on the resulting assemblies.
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Mohammadmehdi Saberioon / S2_Downloader
European Union Public License 1.2Guideline for downloading Sentinel-2 images
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This repository contains a Snakemake workflow tailored for assembling bacterial genomes from long-read data generated with R10.4.1 simplex reads from Oxford Nanopore Technologies and includes several QC steps on the resulting assemblies.
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ILVO-Genomics / GBS / GBS_Trichoderma
MIT LicenseThis code repository stores the code that was used to process Genotyping-by-Sequencing data from Trichoderma asperellum.
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Illumina bacterial assembly snakemake is a snakemake pipeline to assemble lots of bacterial genomes from Illumina paired-end short-reads (typically 150bp); It also performs several QC steps on the reads and on the resulting assemblies. Everything needed can be found in this repository (except for the GTDB reference database for taxonomic assembly classification and the Kraken2 database for taxonomical read classification).
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Steve Baeyen / Bacterial assembly QC snakemake
MIT LicenseThis repository contains a Snakemake bacterial assembly QC pipeline to perform quality control. It will use Quast (metrics), CheckM2 (completedness and contamination), Busco (completedness), skANI (taxonomic assignment against GTDB with ANI). It will also produce a Busco plot summary, a beeswarm plot of N50 and number of contigs, and an excel file with Quast, CheckM2 and skANI summaries.
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Illumina bacterial assembly snakemake is a snakemake pipeline to assemble lots of bacterial genomes from Illumina paired-end short-reads (typically 150bp); It also performs several QC steps on the reads and on the resulting assemblies. Everything needed can be found in this repository (except for the GTDB reference database for taxonomic assembly classification and the Kraken2 database for taxonomical read classification).
Updated -
This repository contains a Snakemake bacterial assembly QC pipeline to perform quality control. It will use Quast (metrics), CheckM2 (completedness and contamination), Busco (completedness), skANI (taxonomic assignment against GTDB with ANI). It will also produce a Busco plot summary, a beeswarm plot of N50 and number of contigs, and an excel file with Quast, CheckM2 and skANI summaries.
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Steve Baeyen / run_epcr
MIT LicenseUpdated -
Plant Modelling / LNPr
GNU General Public License v3.0 onlyUpdated -
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