neat

Simulate sequencing reads using NEAT

usage

nexus run --nf-workflow sequencing_simulation_neat.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_neat "-R 151 -c 30.0 -p 2 --pe 300 30"

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.
--params_neat	Neat parameters (default: “-R 151 -c 30.0 -p 2 –pe 300 30”).
--min_contig_length	Minimum contig length (default: 1000).