Output

This document describes the output produced by the pipeline.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

• FastQC - read quality control

• Sourmash sketch - Compute a k-mer sketch of each sample

• Sourmash compare - Compare all samples on k-mer sketches

• MultiQC - aggregate report, describing results of the whole pipeline

FastQC

FastQC gives general quality metrics about your reads. It provides information about the quality score distribution across your reads, the per base sequence content (%T/A/G/C). You get information about adapter contamination and other overrepresented sequences.

For further reading and documentation see the FastQC help.

NB: The FastQC plots displayed in the MultiQC report shows untrimmed reads. They may contain adapter sequence and potentially regions with low quality. To see how your reads look after trimming, look at the FastQC reports in the trim_galore directory.

Output directory: results/fastqc

• sample_fastqc.html
  • FastQC report, containing quality metrics for your untrimmed raw fastq files
• zips/sample_fastqc.zip
  • zip file containing the FastQC report, tab-delimited data file and plot images

Sourmash Sketch

Sourmash is a tool to compute MinHash sketches on nucleotide (DNA/RNA) and protein sequences. It allows for fast comparisons of sequences based on their nucleotide content.

Output directory: results/sourmash/sketches

For each sample and provided molecule, ksize and log2_sketch_size, a file is created:

• sample_molecule-$molecule_ksize-$ksize_log2sketchsize-$log2_sketch_size.sig

For example:

SRR4050379_molecule-dayhoff_ksize-3_log2sketchsize-2.sig
SRR4050379_molecule-dayhoff_ksize-3_log2sketchsize-4.sig
SRR4050379_molecule-dayhoff_ksize-9_log2sketchsize-2.sig
SRR4050379_molecule-dayhoff_ksize-9_log2sketchsize-4.sig
SRR4050379_molecule-dna_ksize-3_log2sketchsize-2.sig
SRR4050379_molecule-dna_ksize-3_log2sketchsize-4.sig
SRR4050379_molecule-dna_ksize-9_log2sketchsize-2.sig
SRR4050379_molecule-dna_ksize-9_log2sketchsize-4.sig
SRR4050379_molecule-protein_ksize-3_log2sketchsize-2.sig
SRR4050379_molecule-protein_ksize-3_log2sketchsize-4.sig
SRR4050379_molecule-protein_ksize-9_log2sketchsize-2.sig
SRR4050379_molecule-protein_ksize-9_log2sketchsize-4.sig

Sourmash Compare

Output directory: results/sourmash

For each provided molecule, ksize and log2_sketch_size, a file is created containing a symmetric matrix of the similarity between all samples, written as a comma-separated variable file:

• molecule-$molecule_ksize-$ksize_log2sketchsize-$log2_sketch_size.csv

For example,

similarities_molecule-dna_ksize-3_log2sketchsize-2.csv
similarities_molecule-dna_ksize-3_log2sketchsize-4.csv
similarities_molecule-dna_ksize-9_log2sketchsize-2.csv
similarities_molecule-dna_ksize-9_log2sketchsize-4.csv
similarities_molecule-protein_ksize-3_log2sketchsize-2.csv
similarities_molecule-protein_ksize-3_log2sketchsize-4.csv
similarities_molecule-protein_ksize-9_log2sketchsize-2.csv
similarities_molecule-protein_ksize-9_log2sketchsize-4.csv