Rahul Nayak
A Bioinformatician
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WgSim
By Jit 3636 days agogithub.com - Reads simulator Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing...ART: Set of Simulation Tools
By Jit 3503 days agowww.niehs.nih.gov - ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 3111 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
By Jit 3106 days agoftp.genomics.org.cn - An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× simulated pair-end reads from Arabidopsis thaliana with 1% base error. COPE...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 2116 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...Finding a mimicry game for teaching on-line and mentioned general resources
By Shruti Paniwala 1440 days agofinding a mimicry game for teaching on-line and mentioned general resourcesLAMSA: fast split read alignment with long approximate matches
By Jit 2946 days ago Comments (1)github.com - LAMSA (Long Approximate Matches-based Split Aligner) is a novel split alignment approach with faster speed and good ability of handling SV events. It is well-suited to align long reads (over thousands of base-pairs). LAMSA takes takes the...PBSuite: Software for Long-Read Sequencing Data from PacBio
By Jit 3387 days agosourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic...
By Jit 3304 days agogithub.com - This tool is for users to upgrade their metagenomics assemblies using long reads. This includes fixing mis-assemblies and scaffolding/gap-filling. If you encounter any issues, please contact me at kklam@eecs.berkeley.edu. My name is Ka-Kit...Now time is come to revolutionize amino acid sequencing by Nanopore technology
By Rahul Agarwal 4444 days agowww.eurekalert.org - Amino acid sequencing by Nanopore recognition tunneling method
