Host read filtering

Reads mapping to a host genome reference or sequences can be filtered out by specifying the --host_filtering parameter and provide the path to the host fasta file with --host_fasta /path/to/host/fasta/file.

A qc report will be generated summarising the read counts recovered after host filtering.

Introduction

QC step

Preprocessing reads

Host read filtering

Read classification analysis mode

De novo assembly analysis mode

Clustering analysis mode

Mapping to reference analysis mode