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
DISTRUCT: a program for the graphical display of population structure
By Abhimanyu Singh 2081 days agorosenberglab.stanford.edu - distruct is a program that can be used to graphically display results produced by the genetic clustering program structure or by other similar programs. The figures produced by distructdisplay individual membership coefficients...SvABA: Genome-wide detection of structural variants and indels by local assembly
By Abhimanyu Singh 2143 days agogithub.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
By Abhimanyu Singh 2164 days agogithub.com - HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read...Hawkeye: an interactive visual analytics tool for genome assemblies
By Abhimanyu Singh 2164 days agoamos.sourceforge.net - Genome sequencing remains an inexact science, and genome sequences can contain significant errors if they are not carefully examined. Hawkeye is our new visual analytics tool for genome assemblies, designed to aid in identifying and correcting...KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH...
By Abhimanyu Singh 2184 days agowww.kegg.jp - KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data...KEGG Mapper – Reconstruct Pathway
By Abhimanyu Singh 2184 days agowww.kegg.jp - Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome annotations. The input data is a single gene list (for a single organism) or multiple gene lists (for multiple organisms) annotated with KEGG Orthology (KO)...OrthoANI: An improved algorithm and software for calculating average nucleotide identity
By Abhimanyu Singh 2184 days agowww.ezbiocloud.net - OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to...genoPlotR - plot gene and genome maps project!
By Abhimanyu Singh 2184 days agogenoplotr.r-forge.r-project.org - genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files. Features Linear...Genome sequence-based (sub-)species delineation.
By Abhimanyu Singh 2184 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...SISRS: Site Identification from Short Read Sequences
By Abhimanyu Singh 2198 days agogithub.com - Next-gen sequence data such as Illumina HiSeq reads. Data must be sorted into folders by taxon (e.g. species or genus). Paired reads in fastq format must be specified by _R1 and _R2 in the (otherwise identical) filenames. Paired and unpaired reads...
