nanosim-genome

Simulate sequencing reads using NanoSim

usage

nexus run --nf-workflow sequencing_simulation_nanosim-genome.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --model_prefix "" \
    --params_nanosim "--coverage 30 --homopolymer --KmerBias 5"

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.
--model_prefix	NanoSim model prefix.
--params_nanosim	simulator.py genome parameters (default: “–coverage 30 –homopolymer”).