Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data

Hall, M, Coin, L., Pangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data. bioRxiv 2023. doi: [10.1101/2023.09.18.558339][doi]

Benchmarking different ways of doing read (taxonomic) classification, with a focus on removal of contamination and classification of M. tuberculosis reads.

This repository contains the code and ...

BACPAGE

This repository contains an easy-to-use pipeline for the assembly and analysis of bacterial genomes using ONT long-read or Illumina short-read technology. Read the complete documentation and instructions for bacpage and each of its functions here

Introduction

Advances in sequencing technology during the COVID-19 pandemic has led to massive increases in the generation of sequencing data. Many bioinformatics tools ...

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This repository contains an easy-to-use pipeline for the assembly and analysis of bacterial genomes using ONT long-read or Illumina short-read technology.

Introduction

Advances in sequencing technology during the COVID-19 pandemic has led to massive increases in the generation of sequencing data. Many bioinformatics tools have been developed to analyze this data, but very few tools ...

Snakemake workflow: dna-seq-varlociraptor

A ...

ANNOTATO - Annotation workflow To Annotate Them Oll

• ANNOTATO - Annotation workflow To Annotate Them Oll
• Overview of the workflow
• Input data
• Pipeline steps
• Output data
• Prerequisites
• Installation
• Running ANNOTATO
• Before running the pipeline (IMPORTANT) ...

Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data

In recent years, convolutional neural network (CNN)-based methods have shown remarkable performance in the denoising and reconstruction of super-resolved structured illumination microscopy (SR-SIM) data. Therefore, CNN-based architectures have been the main focus of existing studies. Recently, however, an alternative and highly competitive deep learning architecture, ...

A pipeline for mapping, calling, and annotation of SARS-CoV2 variants.

A workflow for mapping and consensus generation of SARS-CoV2 whole genome amplicon nanopore data implemented in the Nextflow framework. Reads are mapped to a reference genome using Minimap2 after trimming the amplicon primers with a fixed length at both ends of the amplicons using Cutadapt. The consensus is called using Pysam based on a majority read support threshold per position of the Minimap2 alignment and positions with less than 30x coverage are masked using ‘N’.

covid-sequence-analysis-workflow

This is the official repository of the SARS-CoV-2 variant surveillance pipeline developed by Danish Technical University (DTU), Eotvos Lorand University (ELTE), EMBL-EBI, Erasmus Medical Center (EMC) under the Versatile Emerging infectious disease Observatory (VEO) project. The project consists of 20 European partners. It is funded by the European Commission.

The ...

Galaxy Workflow created on Galaxy-E european instance, ecology.usegalaxy.eu, related to the Galaxy training tutorial "OBIS marine indicators" .

This workflow allows to compute and visualize marine biodiversity indicators from OBIS data.