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hybrid-assembly

Pipeline for hybrid assembly using short and long reads.

This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.

Pipeline overview

The pipeline is built using Nextflow and processes data using some of the following steps, depending on which assembly tool was chosen:

  • FastQC - short read quality control
  • NanoPlot - long read quality control
  • SPAdes - hybrid assembly
  • Canu - long read assembly
  • minimap2 - mapping of short reads to assembly
  • pilon - Polishing of long read assembly using mapped short reads
  • QUAST - Assembly statistics and quality
  • 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.

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

NanoPlot

NanoPlot is a set of scripts to generate quality control statistics and plots for Oxford Nanopore long reads.

Output directory: results/nanoqc

SPAdes

SPAdes is a versatile de novo genome assembly tool that allows to use both short and long reads for assembly.

Output directory: results/spades_results

Canu

Canu is a assembly tool specifically developed for long read technologies.

Output directory: results/canu

minimap2

minimap2 is a versatile mapping tool that can map short and long reads.

Output directory: results/minimap2

pilon

pilon can be used to improve the quality of assemblies generated with long reads using more accurate short reads.

Output directory: results/pilon

MaSuRCA

MaSuRCA uses superreads and megareads to integrate short and long reads for de novo assembly.

Output direcetory: results/masurca

QUAST

QUAST is a tool for assessing quality statistics of genome assemblies.

Output directory: results/quast_results

MultiQC

MultiQC is a visualisation tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in within the report data directory.

Output directory: results/multiqc

  • Project_multiqc_report.html
    • MultiQC report - a standalone HTML file that can be viewed in your web browser
  • Project_multiqc_data/
    • Directory containing parsed statistics from the different tools used in the pipeline

For more information about how to use MultiQC reports, see http://multiqc.info