Update README.md

README.md

@@ -5,6 +5,7 @@ This repository contains the scripts and pipeline that reproduces the results of
 
 In this benchmarking study: variants callers `BCFtools` (v1.9), `VarScan` (v2.4.3), `Freebayes` (v1.2.0), `LoFreq` (v2.1.3.1), `CLC Genomics Workbench` (v11.0.1) were evaluated. For the assembly benchmarking, `ABySS` (v2.1.4), `megahit` (v1.1.3) , `IDBA` (v1.1.3), `SPAdes` (v3.12.0), `Ray` (v2.3.1), `Tadpole` (v37.99) were assessed. The haplotype reconstruction program `Savage` (v0.4.0) was also evaluated. 
 
+
 ### Prerequirements
 
 To reproduce the output, you need to use `Bioconda`.
@@ -65,7 +66,6 @@ threads: 2 # number of cores to use
 runOnReads: false # Run the whole analyses on reads. Controlled by the `--slow` option
 ```
 
-
 ### Run the benchmarking
 
 **All evaluation can be launched with `run_benchmark.py`**
@@ -302,3 +302,6 @@ python3 run_benchmark.py vareval -t 10 -c ~/miniconda3/envs \
         -r "<comma-separated list of reference genomes>" \
         -o <output directory>
 ```
+
+### Citation
+Deng ZL, Dhingra A, Fritz A, Götting J, Münch PC, Steinbrück L, Schulz T, Ganzenmueller T, McHardy AC. Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses. Briefings in Bioinformatics. 2020:7. https://doi.org/10.1093/bib/bbaa123