Frequently asked questions
We warmly invite you to read our Help
section too. If you still have some doubts about our tool, please write us from our feedback page
- What input files are supported?
- How many samples can be uploaded and analyzed? How many analysis can be run? Are there any time limits?
- Can I upload multiple files? And multiple samples?
- How long does a typical analysis take?
- Which reference genomes and annotations are available under CoVaCS?
- What is the difference between the single sample procedure and the joint sample procedure?
- What is a study? What's the difference with a project?
- Is it possibile to download the results of my analysis?
- I used the COVACS tool for my project. How can I cite it?
Analysis1. What input files are supported?
2. How many samples can be uploaded and analyzed? How many analysis can be run? Are there any time limits?
The COVACS tool supports:
- short-read data-sets produced by Illumina sequencing platforms (FASTQ)
- several standard file formats (SRA, BAM)
- compressed archives (zip1, tar, gzip, bz or bz2 compression are admitted)
COVACS automatically detects the type of uploaded file and chooses the necessary program to decompress it.
 Warning: compressed archives obtained with Mac OS X require the windows-compatibility flag
3. Can I upload multiple files? And multiple samples?
An account with User
- create up to 2 studies
- upload up to 12 files
- build up to 2 analyses
- run 1 analysis at a time
Each sample has to be uploaded as a single file: you can upload multiple files if you have multiple samples.4. How long does a typical analysis take?
The general rule is: 1 sample = 1 file, no merge operation will be executed by our system.
5. Which reference genomes and annotations are available under CoVaCS?
The amount of time required by an analysis execution is influenced by different factors, such as:
- The amount of files uploaded
- The sequencing region (genome-wide or targeted)
- The number of jobs waiting for execution on our servers
However, you can find an estimated execution time in your analysis monitoring page.
Currently it is possible to execute analysis regarding Homo sapiens, Mus musculus and Bos taurus.6. What is the difference between the single sample procedure and the joint sample procedure?
CoVaCS provides pipelines for both joint- (jsp) and single-sample (ssp) variant calling procedures. The jsp procedure allows analysis of a batch of samples, integrating population or pedigree information in the prediction of variants. Joint analysis typically exhibits improved sensitivity for low frequency variants as well as improved specificity at loci with low sequence coverage. Genotype calls are emitted for all loci where at least one individual in the cohort is polymorphic [Van der Auwera et al 2013
], facilitating direct comparison of genotypes. The ssp workflow which employs only data from single individuals, is appropriate for individual and small-scale studies. When resequencing coverage is relatively uniform and of adequate coverage, ssp procedures show similar sensitivity and specificity to joint-sample calling strategies, although performance can be impaired when these conditions are not satisfied [Nho et al, 2010].
Archive1. What is a study? What's the difference with a project?
According to the EBI/ENA data format standard, a study contains information about the a single sequencing project (more analysis can be run in a single study). So, in practice, a study contains all the information about a project.
Results1. Is it possibile to download the results of my analysis?
Yes, you have two options:
Data browsing and downloading has been optimized with caching/sessioning.
- Downloading the results directly from the analysis monitoring page.
- From the Results page, after applying any filter, with the
While this ensures better performance in page loading,
as a drawback opening different tabs on different samples may lead to data misconfiguration.
Please ensure to filter and download one sample at the time.
Other1. I used the COVACS tool for my project. How can I cite it?
BMC Genomics 201819:120. 5 February 2018. doi: 10.1186/s12864-018-4508-1
CoVaCS: a consensus variant calling system.
Chiara M, Gioiosa S, Chillemi G, D'Antonio M, Flati T, Picardi E, Zambelli F, Horner DS, Pesole G.
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