Rahul Nayak
A Bioinformatician
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AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2299 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2252 days agogithub.com - rHAT is a seed-and-extension-based noisy long read alignment tool. It is suitable for aligning 3rd generation sequencing reads which are in large read length with relatively high error rate, especially Pacbio's Single Molecule Read-time (SMRT)...Shouji: a fast and efficient pre-alignment filter for sequence alignment
By Jit 1845 days agogithub.com - The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration...Caretta – A multiple protein structure alignment and feature extraction suite
By Rahul Nayak 1435 days agowww.bioinformatics.nl - Caretta – a multiple protein structure alignment and feature extraction suite Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments...Seal: SEquence ALignment evaluation suite
By Jit 2515 days agocompbio.case.edu - Seal is a comprehensive sequencing simulation and alignment tool evaluation suite. This software (implemented in Java) provides several utilities that can be used to evaluate alignment algorithms, including: Reading a pre-existing reference...
Convert EnsEMBL GTF to Annotation table (Geneid, GeneSymbol, GeneWiseChrLocation, GeneClass,...
Last updated 2307 days ago by Jitendra NarayanBash Script source: https://gist.github.com/santhilalsubhash/367befcf5216be4b1fd9 Information: This script converts EnsEMBL GTF...fastv - detect virus
By Jit 1077 days agogithub.com - fastv is an ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. It detects microbial sequences from FASTQ data, generates JSON reports and visualizes the result in HTML reports. This tool can be used to detect...Public Databases for Bioinformatics !
By Jit 1340 days agomitra.stanford.edu - https://www.nature.com/articles/s41467-020-17155-yServer Infrastructure: File Server: dhara: Synology 3614 Storage Appliance 4 Core Xeon 108TB disk storage 10Gb ethernet to SCG3 Access atx: dhara:5000 Has btsync server (try it - its much...Ribbon: Visualizing complex genome alignments and structural variation:
By Jit 2550 days agohttp://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...jobTree based python wrapper to run the genome simulation tool suite Evolver
By Jit 2541 days agogithub.com - evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation...
