Assembly and quality¶
Aggregates rules for assembling genomes and performing various quality control checks.
Parameters¶
cov_cutoff
: contigs whose coverage is below this cutoff will be excluded from the final assemblyadapter_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 removedminimum_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 samplereport/contamination/low_coverage_contigs/{sample}.html
: quality control report based on the results of fastqc, trimmomatic, qualimap, quast and prokka for every samplereport/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