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.
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".
Raw data and code for the Genomic Analysis of Singles and Pools (GASP) project - https://doi.org/10.1099/mgen.0.001111
MF1 Research and Innovation website
Microbial co-occurrence network reveals climate and geographic patterns for soil diversity on the planet
Code repository for the support project P_Snoeijs-Leijonmalm_2205
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
Full-length bacterial 16S rRNA marker genes from a diverse wastewater sample set. LaMartina, et al., ASM Resource Announcement, 2022
Arche: a functional-optimized annotator for microbial meta(genomes)
Pipeline for amplicon sequencing projects. OTUs can be build with various methods (usearch,vsearch,uparse,swarm) and classified using the RDP Classifier and SINA. Final output is a BIOM file for downstream processing (Phyloseq/R)
Metabundance: Investigating ARG abundance in metagenomes and linking them to MGEs
Repository for the presentation of work developed by the student Duarte Velho for the UC Project, of the Master in Bioinformatics of the University of Minho, academic year 23-24.
Dockerfile to set up omics DB and preinitialized databases
This repo contains scripts used for the identification of phylogenetic marker genes (PMGs) in assembled metagenomic data. Code is provided for benchmarking this method on sequenced genomes as well as running this analysis on metagenomic data. These scripts are in development.
Client Serive of ARGpore pipeline for the analysis of antibiotic resistance in nanopore reads
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