Rahul Nayak
A Bioinformatician
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gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 2385 days agogithub.com - gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and...
List of generic simulation software/tools/resource with brief description and homepage !!!
Last updated 4559 days ago by JitList of generic simulation software/tools/resource with brief description and homepage ALF A Simulation Framework for Genome Evolution http://www.cbrg.ethz.ch/alfBayesian Serial SimCoal Bayesian Serial SimCoal, (BayeSSC) is a modification of...gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
By Rahul Nayak 2274 days agogithub.com - gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command...Blobsplorer
By Jit 3704 days agonematodes.org - Blobsplorer is a tool for interactive visualization of assembled DNA sequence data ("contigs") derived from (often unintentionally) mixed-species pools. It allows the simultaneous display of GC content, coverage, and taxonomic annotation for...CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
By Jit 2270 days agogithub.com - Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by...PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead...
By Rahul Nayak 2983 days agogithub.com - PERGA - Paired End Reads Guided Assembler PERGA is a novel sequence reads guided de novo assembly approach which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct...UniqueKmer: Generate unique KMERs for every contig in a FASTA file
By Abhi 1692 days agogithub.com - Generate unique k-mers for every contig in a FASTA file. Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands). This tool...List of popular bioinformatics software/tools
By Jitendra Narayan 4768 days ago Comments (28)samtools.sourceforge.net - In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.deepTools
By Martin Jones 4288 days agoUser-friendly tools for the normalization and visualization of deep-sequencing dataComputer simulation of genetic mechanism !!
By Jit 3797 days ago Comments (2)Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing the execution output.
