Code supporting Beitel et al. (2014) regarding strain- and plasmid-level metagenome deconvolution using high-throughput chromosome conformation capture.
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Updated
May 29, 2016 - R
Code supporting Beitel et al. (2014) regarding strain- and plasmid-level metagenome deconvolution using high-throughput chromosome conformation capture.
A simple script to detect chimeric sequences in 16S/18S metagenomic samples.
schema2jsonld is a tool for converting externally exposed metadata to schema.org, json-ld structured documents according to EDMI (EOSC Datasets Minimum Information) metadata guidelines
An end-to-end script to convert Illumina shotgun sequences and metadata into full-blown diversity tables and visualizations.
Repository for the Exam project of group 12 in the course "R for bio datascience".
Workflow for Metagenomics assembly with Long reads And Short reads to recover prokaryotic metagenomics-assembled genomes.
Scripts associated with the article "A genome catalogue of lake bacterial diversity and its drivers at continental scale"
Raw data and code for the Genomic Analysis of Singles and Pools (GASP) project - https://doi.org/10.1099/mgen.0.001111
Microbial co-occurrence network reveals climate and geographic patterns for soil diversity on the planet
Antibiotic Resistance Genes Finding
LongReads is a pipeline that compares intra and inter-genomic variation of the 16S region in bacterial species
NGS4ECOPROD - An easy-to-use conda environment and pipelines for metagenome sequence analysis
Microbiome Study of Lupus Patients
Argo: species-resolved profiling of antibiotic resistant genes in complex metagenomes through long-read overlapping
pangenome metagenomics normlization for specific ids
Precise taxomomic classification system for metagenomic read mapping by using Apache Spark
metaTag: functional and taxonomical annotation of metagenomes through phylogenetic tree placement
Modified dada2 script, used for master's thesis project. Takes fast2 files and outputs ASV table, taxonomy table, phylogenetic tree, and input files for PICRUSt2
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