Rahul Nayak
A Bioinformatician
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SimLoRD: A read simulator for third generation sequencing reads
By Aaryan Lokwani 2854 days agobitbucket.org - SimLoRD is a read simulator for third generation sequencing reads and is currently focused on the Pacific Biosciences SMRT error model. Reads are simulated from both strands of a provided or randomly generated reference sequence. The reference...sim3C: Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
By Jit 2771 days agogithub.com - Required python modules biopython intervaltree numpy scipy tqdm PyYAMLSpines
By Jitendra Narayan 3779 days agowww.broadinstitute.org - Spines Spines is a collection of software tools, developed and used by the Vertebrate Genome Biology Group at the Broad Institute. It provides basic data structures for efficient data manipulation (mostly genomic sequences, alignments,...Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish...
By Jit 2701 days agogithub.com - Run a pipeline processing fast5s to a consensus in a single command. Recommended fixed "standard" and "fast" pipelines. Interchange basecaller, assembler, and consensus components of the pipelines simply by changing the target filepath. Seemless...HiCdat
By Jit 3776 days agogithub.com - HiCdat: a fast and easy-to-use Hi-C data analysis tool HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes,...DeepVariant : an analysis pipeline that uses a deep neural network to call genetic variants from...
By Jit 2333 days agogithub.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 2057 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....The Mills lab
The laboratory is focused on the discovery and analysis of structural variation (SVs) from genomic sequence data. As part of the 1000 Genomes Project and other endeavors, we have helped produce initial fine-scale maps using a variety of SV discovery...PEAR: a fast and accurate Illumina Paired-End reAd mergeR
By Jit 3722 days agowww.exelixis-lab.org - PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the...Sr.Bioinformatics Analyst (NGS) @ OcimumBio
Sr.Bioinformatics Analyst (NGS) Experience Required: 3-5 years of experience No of Positions : Multiple Qualifications: Candidates with minimum qualification as M.Sc Bioinformatics with 3-5 years of experience in Life sciences R&D or...
