Standalone Version of GenomeABC

Benchmarking assemblers involves number of steps like downloading of genome data, creation of genomes, mutated genomes, creation of short reads, comparison of assembles and reference genomes. It is time consuming and CPU intensive, it is nearly impossible if network between two systems is slow. In order to provide problem-free service, we developed a standalone software using visual basic dot net for windows operating system. This have three programs for benchmarking of genome assemblers.

ABCeval: This software allows user to compare assembled and reference genome and compute accuracy of assembled genome. It uses BLAT for computing performance from alignment of contigs to reference genome. It require two files i.e. reference genome file and .psl file produce by BLAT. This software will give the analysis report in terms of N50, total genome covered by the contigs (% of the genome), error rate (%), total contig matches (% of the total contig size sum) and error rate(% of the total contig size sum). With the help of this software quality of assembled genome can be determined. You can download this software from following URL ABCeval and its manual from URL Manual of ABCeval

ABChypo: This software can be used for generation of hypothetical/artificial genome and simulated short reads of hypothetical genome. This data (hypothetical genome and simulated short reads) is important for benchmarking of genome assembler. You can download this software from URL ABChypo and its manual from URL Manual of ABChypo

ABCmutate: This software allows user to mutate a genome, where desired number of nucleotides are mutated. It allows user to specify % number of nucleotide to be mutated in genome. This software also generate simulated short reads for mutated genomes. This dataset (short reads and mutated genome) is important for evaluating a assembler when similar genome is available. You can download this software from URL ABCmutate and its manual from URL Manual of ABCmutate Manual of ABCmutate

Complete package of GenomeABC

User can download the complete package of GenomeABC which contain all the three softwares e.g. ABCeval, ABChypo and ABCmutate. Download GenomeABC