All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- Added script for creating joint/hybrid gold standards
- Added script for creating json metadata of data sets
- Output folder will now be created if it is not present
- (Temporarily?) removed the possibility of using readsimulationwrapper as standalone
- Added default config for long read simulation
- Added docker support
- Added no-replace option for genomes in from_profile (default True)
- Genomes are per default split at N positions
- Added new 2018 taxonomy
- Added changelog!
- Loads of Bugfixes
- Changed libraries for downloading genome (now uses https)
- from_profile now uses ete2 API for NCBI
- Argument parsing now has more helptext
- CAMISIM from_profile prints help if called with no options
- Added new ART error profile (MBARC-26)
- Improved error handling for ftp-retrieval (re-try after timeouts)
- from_profile script to create data sets from BIOM profile
- mapping files for downloading genomes from NCBI
- first merge of the original pipeline, the new read simulators and the from_profile branches
- Reworked config and config sections
- i.e. config file reflects added read simulators
- Zero-abundance genomes are now allowed
- wgsim error rates are not fixed anymore
- Updated readme to reflect current changes
- Removed some assertions which caused CAMISIM to terminate prematurely
- Pipeline for the creation of metagenome data sets
- Version used for the creation of the CAMI 1 data sets
- Added defaults, default config files and files to execute a test run
- Implemented PBsim, NanoSim, wgsim read simulators
- Option to start from distribution files instead of completely de novo
- Folder structure now separates external tools and internal scripts