Rahul Nayak
A Bioinformatician
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Qualimap2: Evaluating next generation sequencing alignment data
By Jit 2824 days agoqualimap.bioinfo.cipf.es - Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like...jtools : more efficient presentation of regression analyses
By Neel 2306 days agocran.r-project.org - This package consists of a series of functions created by the author (Jacob) to automate otherwise tedious research tasks. At this juncture, the unifying theme is the more efficient presentation of regression analyses. There are a number of...Collection of Graph Visualization tools !
By Neel 1227 days agopangenome.github.io - Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation...Kraken: ultrafast metagenomic sequence classification using exact alignments
By Jit 3630 days ago Comments (1)www.ncbi.nlm.nih.gov - Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster...CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R
By Shruti Paniwala 2032 days agogitlab.gwdg.de - CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks...pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file
By Jit 2934 days agogithub.com - pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file...BLAST options, setting and defaults
By Jit 2734 days agowww.arabidopsis.org - BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA...Lifemap
By Jit 3343 days agolifemap-ncbi.univ-lyon1.fr - Lifemap is an interactive tool to explore the WHOLE NCBI TAXONOMY. The concept used in Lifemap is similar to the one used in cartography with tools like Google Maps© or Open Street Maps: exploring is done by zooming and panning. The...D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
By Jit 2916 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...SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.
By Jit 2197 days agosynvisio.github.io - SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images. SynVisio requires two files to run: The simplified gff file that was used as an...
