assemble pipeline

This workflow will simply generate assemblies from paired-end fastq, run basic genome annotation with prokka and assess the quality of both the input reads and the resulting assemblies. This workflow forms the basis for amr, typing and pangenome analysis.

flowchart LR
fastq --> assembly --> annotation --> sequence_assessment
assembly --> speciation
fastq --> sequence_assessment --> report
fastq --> speciation --> report

This pipeline should be used if you would like to generate de novo assemblies from paired-end reads. You can choose from spades, skesa, shovill + skesa or shovill + spades (default)

bohra run assemble -i input_file.tsv -j my_assembly_pipeline -a shovill_skesa

where - -i/--input_file is a tab-delimited file formatted as described here - -j/--job_id is the name of your run. This value will appear on your report. - -a/--assembler is the assembler to use (ONT coming soon)