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SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

Pattnaik S, Gupta S, Rao AA, Panda B - BMC Bioinformatics (2014)

Bottom Line: SInC is capable of generating single- and paired-end reads with user-defined insert size and with high efficiency compared to the other existing tools.SInC, due to its multi-threaded capability during read generation, has a low time footprint.We have come up with a user-friendly multi-variant simulator and read-generator tools called SInC.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bangalore 560100, India. binay@ganitlabs.in.

ABSTRACT

Background: The rapid advancements in the field of genome sequencing are aiding our understanding on many biological systems. In the last five years, computational biologists and bioinformatics specialists have come up with newer, better and more efficient tools towards the discovery, analysis and interpretation of different genomic variants from high-throughput sequencing data. Availability of reliable simulated dataset is essential and is the first step towards testing any newly developed analytical tools for variant discovery. Although there are tools currently available that can simulate variants, none present the possibility of simulating all the three major types of variations (Single Nucleotide Polymorphisms, Insertions and Deletions and Copy Number Variations) and can generate reads taking a realistic error-model into consideration. Therefore, an efficient simulator and read generator is needed that can simulate variants taking the error rates of true biological samples into consideration.

Results: We report SInC (Snp, Indel and Cnv) an open-source variant simulator and read generator capable of simulating all the three common types of biological variants taking into account a distribution of base quality score from a most commonly used next-generation sequencing instrument from Illumina. SInC is capable of generating single- and paired-end reads with user-defined insert size and with high efficiency compared to the other existing tools. SInC, due to its multi-threaded capability during read generation, has a low time footprint. SInC is currently optimised to work in limited infrastructure setup and can efficiently exploit the commonly used quad-core desktop architecture to simulate short sequence reads with deep coverage for large genomes.

Conclusions: We have come up with a user-friendly multi-variant simulator and read-generator tools called SInC. SInC can be downloaded from http://sourceforge.net/projects/sincsimulator.

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Time profiles of the different simulators used. Time elapsed to perform one complete simulation with default options using single core across different simulators. A) For chromosome 22 at 15X B) For human whole genome (hg19) at 5X.
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Figure 3: Time profiles of the different simulators used. Time elapsed to perform one complete simulation with default options using single core across different simulators. A) For chromosome 22 at 15X B) For human whole genome (hg19) at 5X.

Mentions: Given the high-throughput nature of NGS data, generating the bulk of simulated data still remains a time consuming process. Hence, we have implemented a “divide and conquer” approach to the read generation module to reduce the time footprint in generating high coverage data. This property allows user to simulate data at a high coverage (50X – 100X) without inordinate expense of time. SInC can utilize 1 to 4 threads for optimal function. Our comparison was set up based on default use of 1 core ranging upto a maximum utilization of 4 cores in SInC versus the other tools (see Results, Figure 3). Details are provided in the Additional file2.


SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data.

Pattnaik S, Gupta S, Rao AA, Panda B - BMC Bioinformatics (2014)

Time profiles of the different simulators used. Time elapsed to perform one complete simulation with default options using single core across different simulators. A) For chromosome 22 at 15X B) For human whole genome (hg19) at 5X.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3926339&req=5

Figure 3: Time profiles of the different simulators used. Time elapsed to perform one complete simulation with default options using single core across different simulators. A) For chromosome 22 at 15X B) For human whole genome (hg19) at 5X.
Mentions: Given the high-throughput nature of NGS data, generating the bulk of simulated data still remains a time consuming process. Hence, we have implemented a “divide and conquer” approach to the read generation module to reduce the time footprint in generating high coverage data. This property allows user to simulate data at a high coverage (50X – 100X) without inordinate expense of time. SInC can utilize 1 to 4 threads for optimal function. Our comparison was set up based on default use of 1 core ranging upto a maximum utilization of 4 cores in SInC versus the other tools (see Results, Figure 3). Details are provided in the Additional file2.

Bottom Line: SInC is capable of generating single- and paired-end reads with user-defined insert size and with high efficiency compared to the other existing tools.SInC, due to its multi-threaded capability during read generation, has a low time footprint.We have come up with a user-friendly multi-variant simulator and read-generator tools called SInC.

View Article: PubMed Central - HTML - PubMed

Affiliation: Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Electronic City Phase I, Bangalore 560100, India. binay@ganitlabs.in.

ABSTRACT

Background: The rapid advancements in the field of genome sequencing are aiding our understanding on many biological systems. In the last five years, computational biologists and bioinformatics specialists have come up with newer, better and more efficient tools towards the discovery, analysis and interpretation of different genomic variants from high-throughput sequencing data. Availability of reliable simulated dataset is essential and is the first step towards testing any newly developed analytical tools for variant discovery. Although there are tools currently available that can simulate variants, none present the possibility of simulating all the three major types of variations (Single Nucleotide Polymorphisms, Insertions and Deletions and Copy Number Variations) and can generate reads taking a realistic error-model into consideration. Therefore, an efficient simulator and read generator is needed that can simulate variants taking the error rates of true biological samples into consideration.

Results: We report SInC (Snp, Indel and Cnv) an open-source variant simulator and read generator capable of simulating all the three common types of biological variants taking into account a distribution of base quality score from a most commonly used next-generation sequencing instrument from Illumina. SInC is capable of generating single- and paired-end reads with user-defined insert size and with high efficiency compared to the other existing tools. SInC, due to its multi-threaded capability during read generation, has a low time footprint. SInC is currently optimised to work in limited infrastructure setup and can efficiently exploit the commonly used quad-core desktop architecture to simulate short sequence reads with deep coverage for large genomes.

Conclusions: We have come up with a user-friendly multi-variant simulator and read-generator tools called SInC. SInC can be downloaded from http://sourceforge.net/projects/sincsimulator.

Show MeSH