AssembleQCHybrid

This workflow uses output from both paired-end and nanopore sequencing to produce a high quality assembly. Input:

• Raw nanopore fastq files as output from MinKnow. Raw nanopore fastq from "fastq_pass" must be joined. Example:

find /fastq_pass/barcode01 -name '\*fastq.gz' -exec cat {} + > barcode01.fastq.gz \

Output:

• QC report.
• Taxonomic analysis.
• Genome Assembly.
• Genome annotation.

Installation.

Requires conda, openpyxl and snakemake to run.
https://docs.conda.io/en/latest/miniconda.html. https://openpyxl.readthedocs.io/en/stable/.
https://snakemake.readthedocs.io/en/stable/.

Install with git

git clone https://github.com/KMA-Aarhus/AssembleQCHybrid.git

DAG of workflow

How to run

Set up an alias for snakemake to run on slurm:

alias snakeslurm='mkdir -p logs/old; mv logs/*.{err,out} logs/old 2> /dev/null; snakemake --profile configs/slurm --use-conda --conda-frontend mamba'

Navigate to AssemblyQCHybrid directory where the snakefile is.

To run

snakeslurm --config R1="path_to_/R1.fastq" R2="path_to_/R2.fastq" ONT="path_nanopore.fastq"
Optionally, an out_base can be provided. as out_base="output". The workflow will then save output files to this location. Default="output".
If your paired-end reads contain UMIs, specify this using option="UMI"

Additional optional options:
kraken2_db # Location of the kraken2 database. Default="/project/ClinicalMicrobio/faststorage/database/kraken2_20210423"

Output

Output can be found in the specified output directory. Output contains:

• A multi-qc report for all samples in the run. The report contains read statistics, assembly statistics, taxonomic analysis, genome coverage and more.
• One folder per sample.
  • "sample_name"_consensus.fasta: assembled and polished genome
  • "sample_name"_consensus.gff: genome annotations
  • "sample_name"_consensus.gbk: annotated genome in genbank format
  • "sample_name"_kraken2_reads_report.txt: the output from kraken2. The same information can be found in the multi-qc report.
  • Addtional output for debugging can be found in:
    • qc
    • plasmidfinder
    • prokka
    • assembly
    • trimmed
    • sampled