RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Assembly and binning of metagenomes

Assembly and intrahost/low-frequency variant calling for viral samples

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

A proof of concept of RNAseq pipeline

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

ARTIC SARS-CoV-2 workflow and reporting

A bioinformatics best-practice analysis pipeline for epitope prediction and annotation

A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.

Influenza genome analysis Nextflow workflow

Influenza genome analysis Nextflow workflow

Nextflow pipeline for NAb-seq (analyses nanopore sequencing data from hybridomas and single B cells)

Nextflow pipeline for generation of phylogenetic trees to be visualized in Auspice.

Generic viral Illumina sequence analysis pipeline