Workflows

Workflow converts one or multiple bam/cram files to fastq format

CAGE-seq pipeline

Simple bacterial assembly and annotation

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

B and T cell repertoire analysis pipeline with the Immcantation framework.

COVID-19: variation analysis on ARTIC ONT data

This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much ...

COVID-19: variation analysis on WGS PE data

This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.