Rahul Nayak
A Bioinformatician
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Useful Bioinformatics Tools
By Poonam Mahapatra 3038 days ago Comments (1)molbiol-tools.ca - Collections of few handy tools for bioinformatician http://molbiol-tools.ca/Convert.htmfragScaff: Genome Assembly with Contiguity Preserving Transposition
By Jit 2415 days agosourceforge.net - Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro means of generating libraries comprised of 9216 indexed pools, each of which contains thousands of sparsely sequenced long fragments ranging from 5 kilobases to...MIX: Combining multiple assemblies from NGS data
By Rahul Nayak 2421 days agogithub.com - Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices...KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
By Jit 2362 days ago Comments (1)github.com - KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts. The following tools are currently available in KAT: hist: Create an histogram of k-mer occurrences from a sequence file. Adds metadata in...Synima: a Synteny imaging tool for annotated genome assemblies
By Abhimanyu Singh 2246 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...Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
By Rahul Nayak 2198 days agobitbucket.org - Some parts of a genome may have a very high degree of heterozygosity. This causes contigs for both haplotypes of that part of the genome to be assembled as separate primary contigs, rather than as a contig and an associated haplotig. This can be an...MITOS: improved de novo metazoan mitochondrial genome annotation
By Jit 2250 days agomitos.bioinf.uni-leipzig.de - Allows automatic annotation of metazoan mitochondrial genomes. MITOS is a pipeline designed to compute a consistent de novo annotation of the mitogenomic sequences. The software allows for a systematic error screening, the standardisation of gene...Protocol for De novo Genome Assembly using Illumina Reads
By BioStar 1436 days agoIn this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome...
By Jit 2278 days agogithub.com - GRSR is a Tool for Deriving Genome Rearrangement Scenarios for Multiple Uni-chromosomal Genomes. This tool will do the following steps: Step 1. Run mugsy to get multiple sequence alignment results. Step 2 & 3. Extraction of the Coordinates...List of tools frequently used while genome assembly
By BioStar 2162 days agoTo decide which strategy should be our “preferred” genome assembly approach based on data rather than my gut-feeling about the “best assembly” I decided to do some testing with a known “true” reference E Coli K12 MG1655
