Search Results for "genome"

What's next of SOAPdenovo2: MEGAHIT is the formal successor of SOAPdenovo2 MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph http://www.ncbi.nlm.nih.gov/pubmed/25609793 https://github.com/voutcn/megahit Latest Code on GitHub: https://github.com/aquaskyline/SOAPdenovo2 SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed...

Chiu et. al., Genome Research 2014 Cupid is a method for simultaneous prediction of miRNA-target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. We showed that our integrative approach significantly improves on miRNA-target prediction accuracy as assessed by both mRNA and protein level measurements in breast cancer cell lines.

CUSHAW2 is a fast and parallel gapped read alignment to large genomes, such as the human genome. The performance evaluation, by aligning simulated and real datasets to the human genome, shows that CUSHAW2 is consistently among the highest-ranked aligners in terms of alignment quality for both single-end and paired-end alignment, while demonstrating highly competitive speed. Furthermore, our aligner shows good parallel scalability with respect to the number of CPU threads.

quadGT is a software package for the joint genotyping of two parents, child’s normal genome and child’s tumor genome based on sequencing reads aligned to a reference genome.