InSilicoSeq

InSilicoSeq (or iss) is a sequencing simulator producing (relatively) realistic Illumina reads primarily intended for simulating metagenomic samples, although it can be used to produce sequencing data from a single genome.

InSilicoSeq is written in python, and use a kernel density estimation model to model the read quality of real sequencing data.

InSilicoSeq support substitution, insertion and deletion errors. If you don’t have the use for insertion and deletion error a basic error model is provided.

Contents

• Installing InSilicoSeq
  • Using pip
  • Using docker
• Generating reads
  • Required input files
  • Abundance distribution
  • Full list of options
• Creating an Error Model
  • Align you reads against the reference
  • Build the model
  • Full list of options
• iss package
  • Subpackages
  • Submodules
  • iss.abundance module
  • iss.app module
  • iss.bam module
  • iss.generator module
  • iss.modeller module
  • iss.util module
  • Module contents

Indices and tables

• Index
• Module Index
• Search Page

This documentation was generated on 2017-11-20 at 09:59.