Rahul Nayak
A Bioinformatician
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The "Ifs" and "Buts" of NGS Quality Control and Trimming
By BioStar 521 days agoNGS quality control and trimming are essential steps to ensure reliable and accurate data for analysis. While the "ifs" highlight the clear benefits of these steps, the "buts" remind us of the potential pitfalls. By adopting best practices and...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By BioJoker 2623 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...LSC :a long read error correction tool
By Jit 2866 days agowww.healthcare.uiowa.edu - Getting Started These simple steps will help you integrate LSC into your transcriptomics analysis pipeline. Read the LSC_requirements for running LSC. Download and set-up the LSC package. Follow the tutorial to see how...Genome assembly tutorial "Genome Assembly for short and long reads"
By Jit 2696 days ago Comments (1)bioinformaticsdotca.github.io - In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs and analysis of the results. At the end of the lab you will...Shasta long read assembler
By Jit 2336 days ago Comments (1)github.com - The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. Computational methods used by the Shasta assembler include: Using...AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads
By Rahul Nayak 1911 days agogithub.com - AlignGraph2 is the second version of AlignGraph for PacBio long reads. It extends and refines contigs assembled from the long reads with a published genome similar to the sequencing genome. More...LRCstats: Long Read Correction Statistics
By Jit 3075 days agogithub.com - LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences. The reads produced by third generation...HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
By Abhimanyu Singh 2714 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...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 2918 days agojapsa.readthedocs.io - npScarf (jsa.np.npscarf) is a program that connect contigs from a draft genomes to generate sequences that are closer to finish. These pipelines can run on a single laptop for microbial datasets. In real-time mode, it can be integrated with simple...1mb long DNA with Nanopore technology
By Jit 3092 days agoLongest read of 1mb achievements with Nanopore
