Jit
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LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2949 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...PureCN: copy number calling and SNV classification using targeted short read sequencing
By Jit 2978 days agobioconductor.org - This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with...Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 3231 days agoschatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...npScarf: real-time scaffolder using SPAdes contigs and Nanopore sequencing reads
By Shruti Paniwala 3037 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...Katuali is a flexible consensus pipeline implemented in Snakemake to basecall, assemble, and polish...
By Jit 2812 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...poRe: an R package for the visualization and analysis of nanopore sequencing data
By Jit 3237 days ago Comments (1)academic.oup.com - Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the...NanoPack: visualizing and processing long-read sequencing data
By Jit 2976 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...Live Webinar on RNA-Seq Data Analysis on 9 Nov 2016
By Strand 3637 days agoLive Webinar on RNA-Seq Data Analysis Abstract: Strand NGS supports an extensive workflow for the analysis and visualization of RNA-Seq data. The workflow includes Transcriptome / Genome alignment, Differential expression analysis with Statistical...GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
By Abhimanyu Singh 3421 days agogithub.com - GRASS (GeneRic ASsembly Scaffolder)-a novel algorithm for scaffolding second-generation sequencing assemblies capable of using diverse information sources. GRASS offers a mixed-integer programming formulation of the contig scaffolding problem, which...VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2921 days agogithub.com - VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store...
