InSilicoSeq

InSilicoSeq simulates realistic Illumina-like sequencing reads for amplicon-based sequencing to enable design and validation of sequencing experiments and benchmarking of bioinformatic workflows.

Key Features:

• Amplicon-based sequencing simulation: InSilicoSeq supports simulation of amplicon-based sequencing reads.
• Premade error models: The software includes premade error models of various quality levels for Illumina MiSeq, HiSeq, NovaSeq and NextSeq platforms.
• Custom error model generation: Users can generate custom error models for any short-read sequencing platform from a BAM-file.
• Adaptive Immune Receptor Repertoire simulation: The amplicon sequencing algorithm can simulate AIRR reads.
• High-throughput performance: InSilicoSeq generated 15 million amplicon-based paired-end reads in under an hour.

Scientific Applications:

• Sequencing experiment design and validation: Simulating reads that mimic empirical sequence data enables designing and validating sequencing experiments prior to actual sequencing.
• Bioinformatic workflow benchmarking: Simulated reads allow for benchmarking of bioinformatic workflows and tools.
• AIRR sequencing simulation: The tool can simulate Adaptive Immune Receptor Repertoire reads for immunological research.

Methodology:

InSilicoSeq uses an amplicon sequencing algorithm to generate reads, with error models derived from empirical data that produce Phred-scores closely resembling actual Illumina MiSeq, HiSeq, NovaSeq and NextSeq sequencing data. Custom error models can be generated from BAM-files.