From 19ac7bd8fb10aecb1345d74bf92ef51b3ba01846 Mon Sep 17 00:00:00 2001 From: Alexis CRISCUOLO <alexis.criscuolo@pasteur.fr> Date: Sun, 8 May 2022 17:36:47 +0200 Subject: [PATCH] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 5f2faed..462ebcf 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ Given one or several [FASTQ](https://en.wikipedia.org/wiki/FASTQ_format) file(s) _ROCK_ can therefore be used to reduce and/or homogenize the overall coverage depth within large sets of HTS reads, which is often required to quickly infer accurate _de novo_ genome assemblies (e.g. Desai et al. 2013, Chen et al. 2015). _ROCK_ can also be used to discard low-covering HTS reads, as those ones are often artefactual, highly erroneous or contaminating sequences. - +For more details, see the associated publication: Legrand et al. (2022) [](https://doi.org/10.21105/joss.03790) ## Compilation and installation @@ -305,6 +305,8 @@ Durai DA, Schulz MH (2019) _Improving in-silico normalization using read weights Kokot M, Długosz M, Deorowicz S (2017) _KMC 3: counting and manipulating k-mer statistics_. **Bioinformatics**, 33(17):2759-2761. [doi:10.1093/bioinformatics/btx304](https://doi.org/10.1093/bioinformatics/btx304). +Legrand V, Kergrohen T, Joly N, Criscuolo A (2022) _ROCK: digital normalization of whole genome sequencing data_. **Journal of Open Source Software**, 7(73):3790. [doi:10.21105/joss.03790](https://doi.org/10.21105/joss.03790). + Liu B, Shi Y, Yuan J, Hu X, Zhang H, Li N, Li Z, Chen Y, Mu D, Fan W (2013) _Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects_. **arXiv**:[1308.2012v2](https://arxiv.org/abs/1308.2012v2). Melsted P, Halldórsson BV (2014) _KmerStream: streaming algorithms for k-mer abundance estimation_. **Bioinformatics**, 30(24):3541-3547. [doi:10.1093/bioinformatics/btu713](https://doi.org/10.1093/bioinformatics/btu713). -- GitLab