Rahul Nayak
A Bioinformatician
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CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
By Shruti Paniwala 1385 days agogitlab.com - CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2857 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
By BioStar 2032 days agogithub.com - SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes...SeqMule: Automated human exome/genome variants detection
By BioStar 2213 days agodoc-openbio.readthedocs.io - SeqMule takes single-end or paird-end FASTQ or BAM files, generates a script consisting of more than 10 popular alignment, analysis tools and runs the script line by line. Users can change the pipeline or fine-tune the parameters by modifying its...
Is reference genome necessary for gene expression study in transcriptome sequencing or for variant discovery in genome sequencing?
Rahul Agarwal 4620 days agoLAPTI Lab
The main theme of our research is the understanding of how genetic information is decoded from DNA into RNA and proteins. Someone may find this topic a little strange and argue that we already know how this is happening. Translational recoding....MIT Computational Biology Group
My research group consists primarily of computer science graduate students and postdocs with expertise in algorithms, statistical inferences and machine learning, and sharing a passion for understanding fundamental biological problems. We work in...
Genome Assembly Tools and Software - PART2 !!
Last updated 3361 days ago by JitThe genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for...P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
By BioStar 2742 days agowww.fishbrowser.org - P_RNA_scaffolder is a novel scaffolding tool using Pair-end RNA-seq to scaffold genome fragments. The method is suitable for most genomes. The program could utilize Illumina Paired-end RNA-sequencing reads from target speciesies. Our method provides...
