Abhimanyu Singh
A bioinformatics beginner
Latest comments
- Jit on Patterns: a modeling tool dedicated to biological network modeling (1956 days ago): https://github.com/fbertran/Patterns
- Abhimanyu Singh on Genome Assembly Tutorial (2906 days ago): This totorial is also very...
- Jit on Next generation sequencing(NGS) books (3766 days ago): Few next generation sequencing resources at...
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Bioinformatics, Genome, NGS, Assembly, Tool, Analysis, Alignment, Genomes, Reads, Read, long, Sequencing, Synteny, Assembler, PacBio, Ancestral, KEGG, Genes, Assemblies, Algorithm, Pipeline, RNA, sequence, annotation, Graph, Books, Lastz, Reference, Mapping, Tutorial, Reconstruction, Format, View, Genomic, Short, Sequences, plot, Gene, Maps, Bacteria, Visual, correction, Variants, Structure, structural, modeling, Method, DISCOVAR, BroadInstitute, SPAdes
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Abhimanyu Singh's bookmarks
karyoploteR: plot whole genomes with arbitrary data
By Abhimanyu Singh 2497 days agobernatgel.github.io - karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...SLIDESORT-BPR
By Abhimanyu Singh 2571 days agogithub.com - Chromosomal rearrangement events are caused by abnormal breaking and rejoining of DNA molecules. They are responsible for many of the cancer related diseases. Detecting the DNA breaking and repairing mechanism, therefore, may offer vital clues about...DiscoSnp
By Abhimanyu Singh 2571 days agogithub.com - DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads. The number of input read sets is not constrained, it can be one, two, or more. No reference genome is...GView: A Java application for viewing and examining prokaryotic genomes in a circular or linear...
By Abhimanyu Singh 2700 days agowww.ncbi.nlm.nih.gov - GView is a Java application for viewing and examining prokaryotic genomes in a circular or linear context. It accepts standard sequence file formats and an optional style specification file to generate customizable, publication quality genome maps...CoreTracker, a codon reassignment tracker
By Abhimanyu Singh 2715 days agogithub.com - CoreTracker detects evidences of codon reassignment from the protein repertoire of a set of genomes by successively applying different algorithms. It’s a filtering approach that explore all possible reassignments in every genomes from the...SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology
By Abhimanyu Singh 2752 days agoufmg-simba.sourceforge.net - SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS)...GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 2752 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...maf2synteny
By Abhimanyu Singh 2757 days agogithub.com - A tool for converting for recovering synteny blocks from multiple alignment (in MAF fromat) This tool is a standalone version of Ragout module [http://fenderglass.github./Ragout]progressiveCactus
By Abhimanyu Singh 2757 days agogithub.com - Progressive Cactus is a whole-genome alignment package. Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules https://github.com/glennhickey/progressiveCactusANGES: reconstructing ANcestral GEnomeS maps
By Abhimanyu Singh 2757 days agopaleogenomics.irmacs.sfu.ca - This page contains the software ANGES 1.01, that aims at reconstucting ancestral genome maps from homologous markers in extant related genomes. Download Program, version 1.01 (July 10, 2012, documentation updated in August 2014) Examples...
