R scripts used for analysis of data reported in Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls

The impact of transitive annotation on the training of taxonomic classifiers

This is an automatic pipeline for analysis of amplicon sequence data including 16S, 18S and ITS. It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UP ARSE, alignment filtering with Gblock, removing Chloroplast sequen…

Primer scripts to produce meaningful visualisations from pre-processed metabarcoding data

Docs for AmpliPiper, developed by @nhmvienna

This is repository of amplicon sequencing data and bioinformatics pipeline codes for the nectar microbiome of Monkey Flowers.

Here we discuss strategies and workflows to analyse metagenomics datasets

QIIME2 worklflow. From raw data to a feature table.

This is a 16S amplicon analysis for visualizing microbiome data using QIIME, QIIME2R and Phyloseq. DNA was isolated fom both sediment cores and seabird fecal samples for this analysis.

Utilities for analysis of multiplex amplicon sequencing data

Code associated with the following manuscript, currently in review: M.S. Fischer, N.J. Patel, P.J. De Lorimier, M.F. Traxler "Prescribed fire selects for a pyrophilous soil subcommunity in a northern California mixed conifer forest"

Metabarcoding pipeline

This pipeline reconstructs the composition of species from 16S amplicon sequencing datasets.

A snakemake pipeline for amplicon (16S, 18S, ITS) sequence analysis using Usearch.

Course repository for Environmental microbiology course (MMB-117) at the University of Helsinki.

Building a pipeline for automated 16S analysis from paired short-reads or long-reads

This repository contains R scripts for data analyses and visualization.

metagenome simulation for targeted and reduced-representation sequencing

CRISPRSeqSim is a tool that simulates results of CRISPR/cas editing fragments target sequencing.

Tesis licenciatura "Metataxonómica de bacterias comoindicador de la descarga de xenobióticos por el Anillo de Cenotes en el sedimento de manglar rojo"