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avantonder/assembleBAC-ONT: Output

Introduction

This document describes the output produced by the assembleBAC-ONT pipeline. The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.

Pipeline overview

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

Nanopore: artic guppyplex

artic guppyplex is used to perform length filtering of the demultiplexed Nanopore reads obtained per barcode.

Output files
  • guppyplex/
    • *.fastq.gz files generated by aggregate pre-demultiplexed reads from MinKNOW/Guppy. These files are not saved by default but can be via a custom config file such as the one below.

Filter long reads

Filtlong is used to filter short reads from Oxford Nanopore FASTQ files.

Output files
  • filtlong/
    • *.log log files generated by Filtlong.

Read Subsampling

rasusa is used to subsample reads to a depth cutoff of a default of 100.

Output files
  • rasusa/
    • *.fastq.gz subsampled fastq files

Remove adapter sequences

(Porechop) is used to remove adapter sequences from Oxford Nanopore reads.

Output files
  • porechop/
    • *.trim.fastq.gz adapter trimmed fastq files

de novo genome assembly

Flye assembles bacterial isolate genomes from Oxford Nanopore reads.

Output files
  • flye/
    • *_log: Flye log files

Sequence Type assignment

mlst is used to assign Sequence Types (STs) to bacterial isolate genomes.

Output files
  • mlst/
    • *.tsv: MLST calls in tsv format
  • metadata/
    • mlst_summary.tsv: mlst summary in tsv format

Genome annotation

Bakta is used for the annotation of bacterial genomes (isolates, MAGs) and plasmids.

Output files
  • bakta/
    • *.gff3: Annotations & sequences in GFF3 format

Genome completeness

CheckM2 is used for the rapid assessment of genome bin quality using machine learning

Output files
  • checkm2/
    • *.tsv: CheckM2 output in tsv format
  • metadata/
    • checkm2_summary.tsv: CheckM2 summary in tsv format

Assembly metrics

Quast is a quality assessment tool for genome assemblies.

Output files
  • metadata/
    • transposed_report.tsv: Quast summary in tsv format

MultiQC

MultiQC is a visualization 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 the report data directory.

Output files
  • multiqc/
    • multiqc_report.html: a standalone HTML file that can be viewed in your web browser.
    • multiqc_data/: directory containing parsed statistics from the different tools used in the pipeline.
    • multiqc_plots/: directory containing static images from the report in various formats.

Pipeline information

Output files
  • pipeline_info/
    • Reports generated by Nextflow: execution_report.html, execution_timeline.html, execution_trace.txt and pipeline_dag.dot/pipeline_dag.svg.
    • Reports generated by the pipeline: pipeline_report.html, pipeline_report.txt and software_versions.yml. The pipeline_report* files will only be present if the --email / --email_on_fail parameter's are used when running the pipeline.
    • Reformatted samplesheet files used as input to the pipeline: samplesheet.valid.csv.

Nextflow provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage.