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Niel Verbrigghe / SoilHydro
MIT LicenseUpdated -
Niel Verbrigghe / alaambak
GNU General Public License v3.0 onlyUpdated -
ILVO-Genomics / SMAP-package / SMAP
GNU Affero General Public License v3.0Updated -
Plant Modelling / LNPr
GNU General Public License v3.0 onlyUpdated -
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hydras / ert-paper
OtherScripts and notebooks for the paper: https://doi.org/10.5194/egusphere-2024-2082
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Plant Modelling / AquacropOnR
MIT LicenseUpdated -
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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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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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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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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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.
Updated -
Updated
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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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ILVO-Genomics / GBS / GBS_Fol4
MIT LicenseUpdated -
Tracking using multiple camera's
Cybele Demo 7#3: carcass tracking
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