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ARC: pipeline which facilitates iterative, reference guided de novo assemblies
By Jit 2782 days agoibest.github.io - ARC is a pipeline which facilitates iterative, reference guided de novo assemblies with the intent of: Reducing time in analysis and increasing accuracy of results by only considering those reads which should assemble...NovoGraph: building whole genome graphs from long-read-based de novo assemblies
By Jit 2669 days agogithub.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 2380 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAPLiftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 2076 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
By Neel 1389 days agogithub.com - The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is...LSC :a long read error correction tool
By Jit 2775 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...LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq...
By LEGE 1633 days agogithub.com - The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed...TULIP - The Uncorrected Long read Itegration Pipeline
By Jit 3026 days agogithub.com - #Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional...TULIP - The Uncorrected Long read Integration Pipeline
By Jit 2854 days agogithub.com - TULIP currently consists of two Perl scripts, tulipseed.perl and tulipbulb.perl. These are very much intended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long...Bioinformatics tools developed for Oxford Nanopore data analysis !
By biogeek 2992 days ago Comments (2)One of the technical advantages of ONT data is the read length, which offers great prospects for genome assembly.
