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.

NonobeseBP

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

pangenome metagenomics normlization for specific ids

Metagenomic toolbox / Outils de métagénomique

Argo: species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping

Kraken2.0.7-beta edited

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

MGnify combined gene caller tool

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

Arche: a functional-optimized annotator for microbial meta(genomes)

🦠💻Operational taxonomic units calculation with abundance greedy clustering🧬🔄

application of expression basedneural network to metagenomics

metegnome sequence extractions from MAGs

Code repository for the support project P_Snoeijs-Leijonmalm_2205