Rahul Nayak
A Bioinformatician
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Bioinformatics Services / CRO Services
Last updated 2313 days ago by RASA Life SciencesRASA is set to provide premium technical and scientific services in a form of solutions, product development and training. .We are also very proficient in providing the high quality Research & Development services in life science informatics...gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 2234 days agogithub.com - gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 2209 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...FiNGS: Filters for Next Generation Sequencing
By Neel 1834 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...-
Libraries or management tools for high throughput sequencing data
Last updated 519 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... -
My commonly used commands in Bioinformatics
Last updated 2781 days ago by Rahul NayakFYI, I've found it useful to use MUMmer to extract the specific changes that Racon makes, so I can evaluate them individually: minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 long_reads.fastq.gz - assembly.fasta... NanoPack: visualizing and processing long-read sequencing data
By Jit 2628 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...Kevler: Reference-free variant discovery in large eukaryotic genomes
By Jit 2230 days agogithub.com - Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based method calls single nucleotide variants (SNVs), multinucleotide variants (MNVs),...RNA-Seq Data Pathway and Gene-set Analysis Workflows
By Jit 4516 days agoDescribe the GAGE workflows on RNA-Seq data pathway analysis and gene-set analysis.BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks
By Rahul Nayak 1903 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...
