Assembly and quality

Aggregates rules for assembling genomes and performing various quality control checks.

_images/assembly.svg

Parameters

  • cov_cutoff: contigs whose coverage is below this cutoff will be excluded from the final assembly
  • adapter_file_name: look for the adaptor for this library preparation kit (possible values)
  • adapter_removal_param1, adapter_removal_param2, adapter_removal_param3: parameters for adapter trimming (reference)
  • minimum_quality_base: leading and trailing bases below this quality will be removed
  • minimum_read_length: reads shorter than this threshold after trimming will be discarded (be careful when using reads from SRA!)

Deliverables

Assembly quality

  • report/multiqc_assembly/multiqc_report.html: quality control report based on the results of fastqc, trimmomatic, qualimap, quast and prokka for every sample
  • report/contamination/low_coverage_contigs/{sample}.html: quality control report based on the results of fastqc, trimmomatic, qualimap, quast and prokka for every sample
  • report/multiqc_assembly/multiqc_report.html: quality control report based on the results of fastqc, trimmomatic, qualimap, quast and prokka for every sample

Assembly and annotation

  • samples/{sample}/assembly/spades/: folder containing all files from SPADES assembly (contigs.fasta, assembly_graph.fastg, contigs.paths,…)
  • samples/{sample_name}/annotation/: folder containing all annotation files from prokka