amplicon-consensus

A simple pipeline for generating a consensus sequence from amplicon-based libraries.

This pipeline is intended as a simple and generic tool for exploring and assessing amplicon-based library preparations. It is not intended to provide final outputs for any specific genomic assay.

This pipeline allows users to quickly and simply assess:

• Depth of coverage across the genome, or specific target region(s)
• Quality of the alignment, including estimates of sequence error rates
• Similarity between generated consensus sequence and a reference.

flowchart TD
  ref[ref.fa]
  bed[scheme.bed]
  fastq[fastq]
  fastq --> fastp(fastp)
  ref --> bwa(bwa_mem)
  fastp -- trimmed_reads --> bwa
  bwa -- alignment --> trim_primer_seqs(trim_primer_sequences)
  bed --> trim_primer_seqs
  trim_primer_seqs -- primertrimmed_alignment --> make_consensus(make_consensus)
  make_consensus -- consensus --> align_consensus_to_ref(align_consensus_to_ref)
  ref --> align_consensus_to_ref

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Usage

The following command can be used to run the pipeline:

nextflow run BCCDC-PHL/amplicon-consensus \
  -profile conda \
  --cache ~/.conda/envs \
  --fastq_input /path/to/fastq_files \
  --ref /path/to/ref.fa \
  --bed /path/to/primer_scheme.bed \
  --outdir /path/to/output_dir

By default, reads will be trimmed by fastp prior to alignment. To align the untrimmed reads instead, use the --align_untrimmed_reads parameter:

nextflow run BCCDC-PHL/amplicon-consensus \
  -profile conda \
  --cache ~/.conda/envs \
  --fastq_input /path/to/fastq_files \
  --ref /path/to/ref.fa \
  --bed /path/to/primer_scheme.bed \
  --align_untrimmed_reads \
  --outdir /path/to/output_dir

If this option is used, the pipeline will proceed as follows, using the original untrimmed reads as input for the bwa alignment process:

flowchart TD
  ref[ref.fa]
  bed[scheme.bed]
  fastq[fastq]
  fastq --> fastp(fastp)
  ref --> bwa(bwa_mem)
  fastq -- untrimmed_reads --> bwa
  bwa -- alignment --> trim_primer_seqs(trim_primer_sequences)
  bed --> trim_primer_seqs
  trim_primer_seqs -- primertrimmed_alignment --> make_consensus(make_consensus)
  make_consensus -- consensus --> align_consensus_to_ref(align_consensus_to_ref)
  ref --> align_consensus_to_ref

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Inputs

Outputs

Coverage Plot