Home

CSReadGen Summary
CSReadGen (V0.1) is an RNA-Seq read simulator that offers a wide range of parameter options. It is designed to allow for the testing of differential expression analysis pipelines, read mapping software and read assembly software. CSReadGen can be used to create a range of read datasets including: (i) A single read dataset where coverage is evenly spread across all transcripts taking length into consideration. (ii) Multiple read datasets, each similar to i, but where the user can specify a range of background count variation. (iii) Multiple read datasets, similar to (ii), but where the user can initially specify a number of transcripts that will have increased counts (simulating increased expression). Within each replicate the selected transcripts will have their count values increased by a factor defined by the user. (iv) Multiple read datasets, similar to (ii), but where the user can initially explicitly specify a number of transcript titles that will have increased counts (simulating increased expression). (v) All of the above with the inclusion of read mismatch and indel error at user specified thresholds( vi) All of the above with the inclusion of a specified percent divergence between reads and the initial reference sets supplied.

Publications

1. Linheiro R, Archer J. CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure. PLOS Comput Biol. 2021;17: e1009631. (view)
2. Linheiro R, Archer J. Quantification of the effects of chimerism on read mapping, differential expression and annotation following short-read de novo assembly. F1000Research 2022 11120. 2022;11: 120. (view)

**Conference(s) **
Posters utilizing CSReadGen to generate test data were presented at ISMB and GenomePT (view poster) as well as at Genomes of Animals& Plants ((view poster)).

Getting Started
The [quickstart] page explains how to run the software as well as the various parameter options available.

Funding
This work was funded by National Funds through Portuguese Foundation for Science and Technology (FCT - Fundac ̧ão para a Ciência e a Tecnologia) and FEDER through the Operational Programme for Competitiveness Factors (COMPETE) under the references POCI-01-0145-FEDER-029115 and PTDC/BIA-EVL/29115/2017.

General detail on this project are available here.

Related Software

1. CStone
2. CSReadGen < (current location)
3. CView
4. ChimSim
5. TVScript

**| linkedIn . web . orcid | **
| linheiro . web . orcid |---| archer . web . orcid |

Licence and Disclaimer

This software is free and open-source software released under the GNU General Public License (GPL).

The software is provided "as is" and without warranty. It may contain errors or produce incorrect results. Users are responsible for evaluating the software and independently verifying any results before relying upon them, particularly for scientific, medical, or other consequential purposes.

To the extent permitted by applicable law, the author accepts no liability for any loss, damage, or other consequence arising from the use of this software.

Java Runtime

The software is intended to run on OpenJDK or another freely available Java Runtime Environment (JRE) or Java Development Kit (JDK) providing the required Java functionality. Compatibility may vary between Java versions and implementations. Third-party libraries or data included with or used by the software may be subject to their own licences and conditions.