Changes for version 0.17 - 2018-05-05

  • Fix bug in fasta_tree and fasta_rtree
  • Populate quality and expression databases
  • Improve documentation
  • Rename project from App-SimulateReads to App-Sandy


A straightforward and complete next-generation sequencing read simulator


App builder that simulates single-end and paired-end reads.
Policy and base module to App::Sandy project.
Base class for command line interface.
App::Sandy::CLI subclass for command line application interface.
App::Sandy::CLI subclass for commands interface
simulate command class. Simulate a custom sequencing
expression command class. Manage expression-matrix database.
expression subcommand class. Add an expression-matrix to the database.
expression subcommand class. Remove an expression-matrix from database.
expression subcommand class. Restore database.
simulate command class. Simulate genome sequencing
quality command class. Manage quality profile database.
quality subcommand class. Add a quality profile to the database.
quality subcommand class. Remove a quality profile from database.
quality subcommand class. Restore database.
simulate command class. Simulate transcriptome sequencing
version command class. Print version
Singleton class to manage database
Class to handle expression-matrix database schemas.
Class to handle quality database schemas.
Base class to simulate fastq entries
App::Sandy::Fastq subclass for simulate paired-end fastq entries.
App::Sandy::Fastq subclass for simulate single-end fastq entries.
Interlaces the processe id for differents processes, actually for parent, child processes.
Class to simulate quality entries
Base class to simulate reads
App::Sandy::Read subclass for simulate paired-end reads.
App::Sandy::Read subclass for simulate single-end reads.
Wrapper on Simulator class for genome/transcriptome sequencing
Input and output custom wrappers.
Getopt::Long wrapper.
Extends class with runtime printf like function
Class responsible to make the simulation
Moose type constraints for App::Sandy project
Weighted raffle interface.