Rahul Nayak
A Bioinformatician
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AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome...
By Jit 2230 days agogithub.com - AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for...FinisherSC: a repeat-aware and scalable tool for upgrading de novo assembly using long reads
By Jit 3299 days agokakitone.github.io - FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high...DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation...
By Jit 3248 days ago Comments (1)github.com - DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies Our work is published in Scientific Reports: Ye, C. et al. DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous...ECTOOLS: Long Read Correction and other Correction tools
By Jit 2987 days agogithub.com - Long Read Correction and other Correction tools This package is a loose collection of scripts. To run the correctionroutine see the section below. Descriptions of the other scriptsare at the bottom of this file. Contact: gurtowsk@cshl.edu In...LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2743 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...NanoSim: nanopore sequence read simulator based on statistical characterization.
By Jit 3005 days agowww.bcgsc.ca - NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides...NanoPack: visualizing and processing long-read sequencing data
By Jit 2770 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...NGS course Medical Genomics, scheduled for 17-20 September 2013 in UZ Leuven (Belgium).
By Poonam Mahapatra 4594 days agoThe 4-day course is organized as a series of morning lectures and afternoon hands-on workshops.
Useful Publications and Websites for Deep Sequencing Data Analysis
Last updated 4454 days ago by Rahul NayakGlobal overview papers Next generation quantitative genetics in plants. Jiménez-Gómez, Frontiers in Plant Science 2:77, 2011 Full Text [equally relevant to animal and microbial systems] Sense from sequence reads: methods for...GABi
GABi Research The major researching fields defined as the GABi scope are described next: Sequence Analysis Protein Structure Prediction Comparative Genomics Functional Analysis of Residues on Protein Families Gene/Protein...
