Poonam Mahapatra
Bioinformatics Researcher
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poRe: an R package for the visualization and analysis of nanopore sequencing data
By Jit 2712 days ago Comments (1)academic.oup.com - Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the...BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing...
By Jit 2523 days agogithub.com - BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a...NanoPack: visualizing and processing long-read sequencing data
By Jit 2451 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 1918 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...NanoPack: visualizing and processing long-read sequencing data
By Jit 2314 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2455 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks
By Rahul Nayak 1589 days agoamp.pharm.mssm.edu - With BioJupies you can produce in seconds a customized, reusable, and interactive report from your own raw or processed RNA-seq data through a simple user interface BioJupies now supports user accounts! Sign in from the top right corner of the page...Powerful books for learning data analysis with R
By LEGE 334 days agohttps://r-graphics.org/ - R is powerful tool for data analysis, visualization, and machine learning. And it costs $0 to use! Here are six FREE books you can use to learn R...McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 1643 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
By BioJoker 2343 days agogithub.com - lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads...
