InSilicoSeq

InSilicoSeq is a sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.

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

InSilicoSeq supports substitution, insertion, deletion errors, and models gc bias and insert size distribution.

Details

• Authors: Hadrien Gourlé, Juliette Hayer, Oskar E. Karlsson and Erik Bongcam-Rudloff
• Contact: hadrien.gourle@slu.se
• GitHub: HadrienG/InSilicoSeq
• License: MIT
• Article: 10.1093/bioinformatics/bty630

Contents

• Installing InSilicoSeq
  • Using pip
  • Using docker
• Generating reads
  • Draft genomes
  • Required input files
  • Abundance distribution
  • Coverage distribution
  • GC bias
  • Basic error model
  • Full list of options
• Error models
  • Pre-built models
  • Creating an Error 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 2021-09-29 at 08:54.