Abhimanyu Singh
A bioinformatics beginner
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- 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
Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life
By Abhimanyu Singh 2224 days agoancestralgenomes.org - Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species...swgis v2.0 : a seqword genomic island sniffer
By Abhimanyu Singh 2225 days agoeugi.bi.up.ac.za - swgis v2.0 is the modified version of the seqword genomic island sniffer. this version is specifically optimized for predicting genomic islands in eukaryotic genomes. swgis v2.0 was tested on several eukaryotic species of different lineages....Synima: a Synteny imaging tool for annotated genome assemblies
By Abhimanyu Singh 2227 days agogithub.com - Synima written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included...VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity
By Abhimanyu Singh 2227 days agowww.ncbi.nlm.nih.gov - VGSC, the Vector Graph toolkit of genome Synteny and Collinearity, and its online service, to visualize the synteny and collinearity in the common graphical format, including both raster (JPEG, Bitmap, and PNG) and vector graphic (SVG, EPS, and...S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences
By Abhimanyu Singh 2254 days agobitbucket.org - S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can...rHAT: a seed-and-extension-based noisy long read alignment tool
By Abhimanyu Singh 2264 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)...LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2280 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2280 days agogite.lirmm.fr - An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are...miREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set
By Abhimanyu Singh 2302 days agobioinfo-csi.nus.edu.sg - From list of genes... ... to microRNAs Using established miRNA-interaction databases, miREM combines hypergeometric and expectation-maximization algorithms to sieve through your genetic data for microRNA...MeDuSa: a multi-draft based scaffolder
By Abhimanyu Singh 2485 days agogithub.com - MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa...
