Rahul Nayak
A Bioinformatician
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Pacbio Long Reads Compatible Software and Tools
By Archana Malhotra 3431 days agogithub.com - The following software packages are known to be compatible with PacBio® data, in addition to PacBio's own SMRT® Analysis suite. All packages are believed to be open source or freely available for non-commercial use. See the individual...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 3195 days agowww.ncbi.nlm.nih.gov - We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...CoLoRMap: Correcting Long Reads by Mapping short reads
By Jit 2908 days agogithub.com - Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies....MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 3010 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By Jit 2978 days agowww.fishbrowser.org - P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs,...
getopts.pl file
By Jit 2975 days agoSSPACE_longread complain for getopts.pl file. To resolve this, download and have in SSPACED-Longreads folder. Cheers :)P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2891 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...HASLR: a tool for rapid genome assembly of long sequencing reads
By LEGE 2380 days agogithub.com - HASLR is a tool for rapid genome assembly of long sequencing reads. HASLR is a hybrid tool which means it requires long reads generated by Third Generation Sequencing technologies (such as PacBio or Oxford Nanopore) together with Next Generation...RagTag: a collection of software tools for scaffolding and improving modern genome assemblies
By Jit 1791 days agogithub.com - RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include: Homology-based misassembly correction Homology-based assembly scaffolding and patching Scaffold mergingPHYMMBL
By Jit 3588 days agowww.cbcb.umd.edu - Metagenomics sequencing projects collect samples of DNA from uncharacterized environments that may contain hundreds or even thousands of species. One of the main challenges in analyzing a metagenome is phylogenetic classification of raw sequence...
