LRTK-SIM

LRTK-SIM simulates 10x Chromium linked-read sequencing to generate realistic linked-read datasets for evaluating and optimizing genome assembly and variant analysis.

Key Features:

• Linked-Read Simulation: Follows the 10x Chromium System data-generation workflow to produce realistic linked-read datasets.
• Haploid and Diploid Simulations: Accepts one or two FASTA files (Path_Fastahap1, Path_Fastahap2) to simulate haploid or diploid genomes and can introduce SNVs using gen_fasta.py.
• Parameter Exploration: Simulates and assesses the effects of total sequencing coverage (C), physical fragment coverage (CF), read coverage per fragment (CR), and length-weighted fragment length (Wμ_FL) on assembly quality.

Scientific Applications:

• Genome Assembly Optimization: Enables evaluation of how different 10x library-preparation and sequencing parameter settings affect de novo and haplotype-resolved genome assembly quality.
• Variant Detection: Provides realistic linked-read datasets for assessing variant discovery and analysis pipelines under varied sequencing scenarios.

Methodology:

Mimics the 10x Chromium System data-generation process; accepts Path_Fastahap1 and Path_Fastahap2 FASTA inputs; introduces SNVs using gen_fasta.py; simulates parameter settings (C, CF, CR, Wμ_FL); and has been applied to datasets from NA12878 and NA24385.