Rahul Nayak
A Bioinformatician
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A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
By Abhimanyu Singh 3373 days agowww.sanger.ac.uk - PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed: ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference. IMAGE, an...HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
By Jit 3102 days agogithub.com - Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.org/content/27/5/747.full An ipython notebook to...SPADes team announce new version SPADes v3.15
By BioStar 2029 days agoNew SPAdes 3.15.0.0. announced by the SPADes teamkWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
By Rahul Nayak 2991 days agogithub.com - The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any...Ribbon: Visualizing complex genome alignments and structural variation:
By Jit 3172 days agohttp://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...Mugsy: multiple whole genome alignment tool
By Jit 3163 days ago Comments (1)mugsy.sourceforge.net - Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee....
