Name: Hisat2 Simulate Reads Py
Author: vimalinx

Quick Start

Command: hisat2_simulate_reads.py [genome_file] [gtf_file] [snp_file] [base_fname]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2_simulate_reads.py
Full reference: See references/help.md for complete options and usage details

When To Use This Tool

Use hisat2_simulate_reads.py when you need synthetic HISAT2-style benchmark reads from a genome, annotation, and SNP set.
It is appropriate for RNA-seq by default, but can also simulate DNA-seq with -d.
Use it when benchmarking alignment settings, validating graph-aware variant handling, or generating controlled test data with fixed read and fragment lengths.
Reach for it when you need reproducible simulations with explicit random seeds and optional sanity checks.

Command: hisat2_simulate_reads.py [genome_file] [gtf_file] [snp_file] [base_fname]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2_simulate_reads.py
Full reference: See references/help.md for complete options and usage details

Use hisat2_simulate_reads.py when you need synthetic HISAT2-style benchmark reads from a genome, annotation, and SNP set.
It is appropriate for RNA-seq by default, but can also simulate DNA-seq with -d.
Use it when benchmarking alignment settings, validating graph-aware variant handling, or generating controlled test data with fixed read and fragment lengths.
Reach for it when you need reproducible simulations with explicit random seeds and optional sanity checks.