pbsim3-dna

Simulate sequencing reads using PBSIM3

usage

nexus run --nf-workflow sequencing_simulation_pbsim3-dna.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --pbsim3_model_file /path/to/file \
    --params_pbsim3_mode "errhmm" \
    --params_pbsim3 "--depth 30 --length-mean 17000 --pass-num 10 --strategy wgs"

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘fasta_file’.
--output_dir	Directory to which output files will be copied.
--pbsim3_model_file	PBSIM3 error model file (ERRHMM*.model).
--params_pbsim3_mode	PBSIM3 mode (default: ‘“errhmm”’). Either ‘“errhmm”’ or ‘“qshmm”’.
--params_pbsim3	PBSIM3 parameters (default: “–depth 30 –length-mean 17000 –length-sd 2000 –pass-num 10 –strategy wgs”).
--min_contig_length	Minimum contig length (default: 1000).