TuneSim







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Welcome to TuneSim


TuneSim allows you to vizualize the results of Escaliere et al. (ref tba) in a user-friendly format (from Panel Simulations cov10 to Panel Illumina Platinum Filtered). TuneSim allows you to test your own pipeline through a very simple procedure (see step-by-step procedure on the Tutorial Panel).
You can evaluate your own pipeline on FastQs from :
- simulated 100 bp paired-end reads with realistic 1KG and dbSNP haplotypic variants insertion and realistic base quality scores (through a meliorated version of dwgsim)
- curated human data from the NA12878 individual (through GiAB or illumina Platinum projects)
The simulated data have different mean coverage allowing you to dynamically stress your pipeline and reveal its possible strengths and weaknesses on 4 different types of variants.
SNPs and indels from dbSNP129, i.e. variants found before any large NGS dataset project; SNPs and indels from dbSNP 130 or later called NOVEL.
Those later dbSNP versions will be plagued by NGS false positives and/or variants more difficult to call.
In its standalone version (add here the gitHub/download link), TuneSim is also able to insert increasing levels of random variants and sequencing errors.
For TuneSim to analyze your results, you will upload your output vcfs (cut on target file ; file size issues) through the left side panel.
Your results will be compared with the rediscovery and false positive rates obtained on the same datasets by standard pipelines as described in Escalière et al. (ref tba).
Your results will be easily vizualized in the Data, Rediscovery Rate and Your Pipeline panels. An export function is available for you to save the results and images.
Hoping it will be useful to some of you,
The TuneSim team.

1) download FastQ files on download Panel (2 files R1 and R2 for paired end)



2) Run your pipeline on FastQ files and cut on target


3) Submit your vcf file and choose your study (simulated (with coverage associated and filtering or not), GIaB or Illumumina Platinum). Indicate your aligner and variant caller(only for plotting consideration).Then launch the computation with compare button.



4) Enjoy TuneSim
5) A pdf report is available using 'download' button
Links to download the different FastQ files :

All the FatsQ files are available here
NIST35 and NIST86 are GIaB files. You can compare them against GIaB and Illumina Platinum in this website. Other files are simulated paired end FastQ, the coverage is mentioned in file names.