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ART: Set of Simulation Tools
By Jit 2944 days agowww.niehs.nih.gov - ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated...SpeedSeq
By Jit 2866 days agogithub.com - A flexible framework for rapid genome analysis and interpretation C Chiang, R M Layer, G G Faust, M R Lindberg, D B Rose, E P Garrison, G T Marth, A R Quinlan, and I M Hall. SpeedSeq: ultra-fast personal genome analysis and interpretation. Nat Meth...GAM-NGS: genomic assemblies merger for next generation sequencing
By Jit 2747 days agogithub.com - GAM-NGS is a tool able to merge two or more assemblies in order to improve contiguity and correctness. It can be used on all NGS-based assembly projects and it shows its full potential with multi-library Illumina-based projects. With more than 20...BBTools for bioinformatician !
By Surabhi Chaudhary 2474 days ago Comments (1)BBTools can do almost everything now !Porechop: tool for finding and removing adapters from Oxford Nanopore reads
By Rahul Nayak 2372 days agogithub.com - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop...AlignQC: A tool for assessing an alignment, and generating reports that are easy to share
By Jit 2302 days agowww.healthcare.uiowa.edu - Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser...Understanding HiFi Reads !
By Rahul Nayak 976 days agopacb.com - While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot...1mb long DNA with Nanopore technology
By Jit 2532 days agoLongest read of 1mb achievements with NanoporeNanoPack: visualizing and processing long-read sequencing data
By Jit 2161 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...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2386 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...
