Rahul Nayak
A Bioinformatician
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Merqury: reference-free quality and phasing assessment for genome assemblies
By Jit 2311 days agogithub.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
By Jit 2061 days agogithub.com - Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz...INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 3233 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2647 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
By Neel 1645 days agogithub.com - Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the...Translational Bioinformatics: Transforming 300 Billion Points of Data
By Jitendra Narayan 4793 days agoTranslational Bioinformatics: Transforming 300 Billion Points of Data into Diagnostics, Therapeutics, and New Insights into Disease Air date: Wednesday, June 20, 2012, 3:00:00 PM Time displayed is Eastern Time, Washington DC Local...ANGES: reconstructing ANcestral GEnomeS maps
By Abhimanyu Singh 3426 days agopaleogenomics.irmacs.sfu.ca - This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes. Download Program, version 1.01 (July 10, 2012, documentation updated in August 2014) Examples...dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
By Jit 3210 days agowww.ncbi.nlm.nih.gov - While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembly of highly polymorphic (HP) diploid genomes remains challenging. As a result, there is a shortage of tools for assembling HP genomes from the...D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
By Jit 3037 days agodgenies.toulouse.inra.fr - D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool designed to compare two genomes. It supports large genome and you can interact with the dot plot to improve the visualisation. We use minimap...Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
By Abhi 872 days agogithub.com - Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia can be split into two main...
