Rahul Nayak
A Bioinformatician
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Genetic code - Amino Acid
By Poonam Mahapatra 3683 days agoThe genetic code consists of 64 triplets of nucleotides. These triplets are called codons.With three exceptions, each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code: most of...Meraculous: De Novo Genome Assembly with Short Paired-End Reads
By Jit 2575 days agowww.ncbi.nlm.nih.gov - We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia...funannotate: Eukaryotic Genome Annotation Pipeline
By Jit 2259 days agogithub.com - Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this...SALSA: A tool to scaffold long read assemblies with Hi-C
By Jit 2355 days agogithub.com - This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version,...Genome sequence-based (sub-)species delineation.
By Abhimanyu Singh 2175 days agohttp://ggdc.dsmz.de/ - The GGDC web service reports digital DDH for a universal and accurate delineation of prokaryotic (sub-)species without inheriting the pitfalls of classic DDH, and also calculates differences in genomic G+C...Roary: the Pan Genome Pipeline
By Jit 2134 days ago Comments (1)sanger-pathogens.github.io - Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of...RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
By BioJoker 2049 days agogithub.com - Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into...List of universities offering Bachelor or Master bioinformatics degree in Pakistan
By Reshma Khatun 2714 days agoThere are a lot of universities offering Bachelor or Master degree in Pakistan. Following are the list of few intitute/universitiesMGSE: Mapping-based Genome Size Estimation
By Shruti Paniwala 1774 days agogithub.com - MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly. The script...U-Plot: Genome U-Plot sample implementation
By Rahul Nayak 1728 days agogithub.com - The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.
