Major Features

Background One of the major challenge in the present era is to assemble genomes from short reads generated by Next Generation sequencing technologies (e.g. Illumina’s Solexa). In past, several assemblers have been developed for assembling genomes from short reads, it is difficult to say which assembler is best as they have been evaluated on different datasets. Thus their is need to develop tools and dataset for benchmarking genome assemblers. This GenomeABC is one important step towards benchmarking of assemblers. Benchmarking of assemblers is important for both users in order to use best assembler and for developers for comparing performance of their newly developed assembler with existing assemblers.

Major Features: Following are major features of this platform

Dataset for Benchmarking: Dataset is most important component of Benchmarking. In this study, we evaluate performance of existing assemblers on one real genome Pseudomonas syringae and four hypothetical genomes. These genomes and their short reads are available for users to download from Data set menu. This will allow users to evaluate their assemblers and compare performance with existing assemblers evaluated in this study.

Benchmarking of Assemblers: In this study we evaluate number of popular genome assemblers. These assemblers were evaluated on genome Pseudomonas syringae and on hypothetical genomes. The comprehensive performance of assemblers is available from Benchmarking of Existing Assemblers.

Benchmarking of New Assembler : This plateform allows users to evaluate a newly developed or assemblers of their choice. Users may evaluate their assembler on Benchmarking Data Set provided on this plateform or on entirely new dataset. User should provide reference genome and contigs generated by assembler. For detail see URL New Assembler

Create a Hypothetical Genome : This platform can be used for generation of artificial genome and simulated reads from that genome so that both i.e. genome and reads both available at the same time. User can use this data to evaluate the performance of a genome assembler. This is important to evaluate de novo assembler. For detail see URL Hypothetical Genome

Create a Muated Genome: This platform provides option to mutate a genome with desired number of mutation in genome. This also allows to generate short reads of mutated genomes. This option is very important to understand performance of assembler on genomes whose similar genomes have already been sequenced. For detail see URL Mutated Genome

Generate Short Reads: On this platform, we are providing a facility by which a user can simply create short reads (Solexa type) for a genome of interest. Reads generated by this server can be assembled and aligned to original genome. This strategy will be helpful for the evaluating performance of genome assembler at different parameters. For detail see URL New Short Reads

Standalone Software: In order to provide service to community, we created this platform. We also realized problems of web server like transfer of huge data time consuming, CPU usage is too high. Thus we also developed standalone version of GenomeABC which can be downloaded from this site Standalone Software . This software will RUN on any PC with MS-Windows.