WORKFLOW: GAEMR

The GAEMR workflow simplifies running GAEMR analysis to assess assembly quality for multiple samples.

Parameter Identifier	Parameter Value Type / Default	Parameter Description
reference_fasta	String. None	Path to reference genome FASTA. In the same directory as the FASTA file should be representative bwa index files. To ensure things run smoothly please run bwa using its installation in the conda environment main_env.
run_subsample	String/Boolean. False	Specify whether to perform subsampling of reads (e.g. to quickly get a glimpse of the data).
read_subsampling	Integer. 10000	The number of reads to subsample.
gaemr_formatter_options	String. -g 1 -c 100 -r	Options for preparing assembly for GAEMR QC analysis.
gaemr_qc_options	String. --force --analyze_rna	Options for GAEMR QC analysis.
gaemr_threads	Integer. 4	The number of cores/threads to run GAEMR using.
gaemr_memory	Integer.16	The memory in (Gb) to provide for each core.
gaemr_timelimit	String. 24:00:00	The timelimit for running GAEMR analysis.
run_cleanup	String/Boolean. False	Delete intermediate FASTQ files: True/False