30  Run bactmap

Learning Objectives
  • Generate consensus genomes for pneumococcus using reference-based aligment.
Remember to QC your sequencing reads

Remember, the first step of any analysis of a new sequence dataset is to perform Quality Control. For the purposes of time, we’ve run bacQC for you and the results are in preprocessed/bacqc. Before you run bactmap, have a look at the read stats and species composition TSV files and make sure that the data looks good before we go ahead and map it.

Exercise: Running nf-core/bactmap

Your next task is to run the bactmap pipeline on the S. pneumoniae data. In the folder scripts (within the S_pneumoniae analysis directory) you will find a script named 01-run_bactmap.sh. This script contains the code to run bactmap.

  • First, create a samplesheet.csv file for bactmap. Refer back to The bacQC pipeline page for how to do this, if you’ve forgotten.

  • Edit the 01-run_bactmap.sh script, adjusting it to fit your input files and the name and location of the reference you’re going to map to (Hint: the reference sequence is located in resources/reference).

  • Activate the nextflow software environment.

  • Run the script using bash scripts/01-run_bactmap.sh.

  • Have a look at the MultiQC report. Do any of the samples look to be poor quality?

First, we created our samplesheet using the helper python script, as explained for the bacQC pipeline:

python scripts/fastq_dir_to_samplesheet.py data/reads \
    samplesheet.csv \
    -r1 _1.fastq.gz \
    -r2 _2.fastq.gz

Next, we fixed the script:

#!/bin/bash

nextflow run nf-core/bactmap \
  -profile singularity \
  --max_memory '16.GB' --max_cpus 8 \
  --input samplesheet.csv \
  --outdir results/bactmap \
  --reference resources/reference/GCF_000299015.1_ASM29901v1_genomic.fna \
  --genome_size 2.0M

Then, we activated the nextflow environment:

mamba activate nextflow

Finally, we ran the script as instructed using:

bash scripts/01-run_bactmap.sh

While it was running it printed a message on the screen:

N E X T F L O W  ~  version 23.04.1
Launching `https://github.com/nf-core/bactmap` [cranky_swartz] DSL2 - revision: e83f8c5f0e [master]


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/bactmap v1.0.0
------------------------------------------------------

The results for all the samples looked really good so we can keep all of them for the next steps of our analyses.

Exercise: How much of the reference was mapped?
  • Activate the seqtk software environment.
  • Run the 02-pseudogenome_check.sh script we’ve provided in the scripts folder, which calculates how much missing data there is for each sample using seqtk comp.
  • Once the analysis finishes, open the mapping_summary.tsv file in Excel from your file browser .
  • Sort the results by the %ref mapped column and identify the sample which has the lowest percentage of the reference mapped.

  • We activated the software environment: mamba activate seqtk

  • We then ran the script using bash scripts/02-pseudogenome_check.sh. The script prints a message while it’s running:

    Processing ERX1265396_ERR1192012.fas
Processing ERX1265488_ERR1192104.fas
Processing ERX1501202_ERR1430824.fas
...

We opened the mapping_summary.tsv file in Excel and sorted the %ref mapped in ascending order to identify which sample had the lowest percentage of the reference mapped.

sample  ref_length  #A  #C  #G  #T  mapped  %ref mapped
ERX1501218_ERR1430840   2064154 593340  394510  390906  593159  1971915 95.53138962
ERX1501224_ERR1430846   2064154 593599  394628  391029  593404  1972660 95.56748188
ERX1501259_ERR1430881   2064154 593659  394622  391027  593434  1972742 95.57145446
ERX1501253_ERR1430875   2064154 593621  394666  391085  593416  1972788 95.57368297
ERX1501207_ERR1430829   2064154 593665  394643  391028  593476  1972812 95.57484568

We can see that ERX1501218_ERR1430840 mapped to 95.5% of the reference which is well above 90% so the mapping worked really well for this set of samples.

30.1 Summary

Key Points
  • Obtaining genomes for a species such as pneumococcus can be done using reference-based alignment.
  • We can use the same workflows and scripts covered so far:
    • avantonder/bacQC to perform sequence quality control on the raw sequencing reads.
    • nf-core/bactmap for generating consensus genome sequences based on mapping reads to a reference genome.
    • Use a custom script to loop through our samples and run seqtk comp, which estimates the fraction of missing data in our genomes.