nf-core/detaxizer
A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.
de-identificationdecontaminationednafastqfilterlong-readsmetabarcodingmetagenomicsmicrobiomenanoporeshort-readsshotguntaxonomic-classificationtaxonomic-profiling
Version history
First release of nf-core/detaxizer!
This is the initial version of the pipeline:
- Read QC (
FastQC
) - Pre-processing (
fastp
) - Classification of reads (
Kraken2
) - Optional validation of searched taxon/taxa (
blastn
) - Optional filtering of the searched taxon/taxa from the reads (either from the raw files or the preprocessed reads, using either the output from kraken2 or blastn)
- Summary of the processes (how many reads were initially present after preprocessing, how many were classified as the
tax2filter
plus potential taxonomic subtree and optionally how many were validated) - Present QC for raw reads (
MultiQC
)