Rahul Nayak
A Bioinformatician
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Choosing the Right NGS Sequencing Instrument for Your Study
By Neel 1363 days agogenohub.com - The right sequencing instrument for your study depends on your project goal. Setting aside turnaround time and price, it essentially comes down to the numbers of reads and read length you need for your experiment. Below, we've described and compared...1mb long DNA with Nanopore technology
By Jit 3002 days agoLongest read of 1mb achievements with NanoporeNanoPack: visualizing and processing long-read sequencing data
By Jit 2630 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible...Understanding your reads and mapping !
By Neel 2231 days agobioinformatics-core-shared-training.github.io - One of the best tutorial for beginners ... https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.htmlINC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 3024 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...TAREAN: A computational tool for identification and characterization of satellite DNA from...
By Surabhi Chaudhary 2855 days agobitbucket.org - TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their...GenomeMapper: Simultaneous alignment of short reads against multiple genomes
By Jit 2845 days ago1001genomes.org - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simulanteously or against a single...Hercules: a profile HMM-based hybrid error correction algorithm for long reads
By Jit 2758 days agogithub.com - Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accurate reads including de novo assembly, fusion and structural variation detection....LoRMA: A tool for correcting sequencing errors in long reads
By Abhimanyu Singh 2741 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...Wtdbg2: a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore
By Neel 2698 days agogithub.com - Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2...
