Rahul Nayak
A Bioinformatician
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Upset plots !
By BioStar 1080 days agojokergoo.github.io - Upset plots are a type of visualization used to analyze the intersection of sets or categories. They are particularly useful for displaying data with multiple categories and analyzing their overlaps. In an upset plot, each row represents a category...
Libraries or management tools for high throughput sequencing data
Last updated 521 days ago by LEGEGATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.These methods enable the analysis of data sets of any size on multi-core desktop...PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
By Surabhi Chaudhary 2828 days agoderisilab.ucsf.edu - We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively...Magic-BLAST: a tool for mapping large next-generation RNA or DNA sequencing runs against a whole...
By Jit 2994 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...chromoMap-An R package for Interactive visualization and mapping of human chromosomes
By Rahul Nayak 2813 days ago Comments (1)An R package for Interactive visualization and mapping of human chromosomesVCF Compare !
By Rahul Nayak 1510 days agowiki.bits.vib.be - compare two BWA mapping methods with the online hg18-mapped data We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep...mrFAST: Micro Read Fast Alignment Search Tool
By Neel 3604 days agomrfast.sourceforge.net - mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold,...Maq: Mapping and Assembly with Quality
By Jit 3394 days agomaq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....BlasR Mapping single molecule sequencing reads using Basic Local Alignment with Successive...
By Jit 2847 days agobix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...FUMA GWAS: Functional Mapping and Annotation of Genome-Wide Association Studies
By Jit 2473 days agohttps://fuma.ctglab.nl/ - FUMA is a platform that can be used to annotate, prioritize, visualize and interpret GWAS results. The SNP2GENE function takes GWAS summary statistics as an input, and provides extensive functional annotation for all SNPs in genomic...
