Assembly Quality Control

subworkflows/local/qc_assembly

Generate assembly quality metrics QUAST is used to generate summary assembly metrics such as: N50 value, number of contigs,average depth of coverage and genome size.
Assembly filtering Using a custom nexflow DSL (Groovy)script, assemblies are filtered to meet quality thresholds.
See nextflow.config in the quast_filter section to see what defaults are currently implemented, or to set your own.
Contamination detection CheckM is run to identify a percent contamination score and build up evidence for signs of contamination in a sample.
CheckM can be skipped by adding --skip_checkm to the command-line options as the data it generates may not be needed, and it can have a long run time.
Classic seven gene MLST mlst is run and its outputs are contained within the final report.
This step can be skipped by adding --skip_mlst to the commmand line options.

cleaned reads (fastq) from the FinalReads dir
This is the final reads file from the last step in the Clean Reads workflow (taking into account any skip flags that have been used)
Contig file (fasta) from the FinalAssembly dir
This is the final contig file from the last step in the CleanAssemble workflow (taking into account any skip flags that have been used)