CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means...2210 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...d server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance. Can run as a stand-alone app on OSX and Windows using the Electr...2201 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
...a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that contain hundreds of...2197 days ago
RNA-seq Analysis Workshop Course Materials
...ed against the reference genome and significantly improves our ability to reconstruct transcripts. This category would obviously include humans and most model organisms but excludes...2197 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
...s. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called red-black multipositional de Bruijn graph to det...2194 days ago
transrate: Understanding your transcriptome assembly
...il and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and param...2187 days ago
ARC: pipeline which facilitates iterative, reference guided de novo assemblies
...time in analysis and increasing accuracy of results by only considering those reads which should assemble...be assembled quickly and efficiently in parallel. Applications include those in which the researcher wish...2174 days ago
nanofilt: Filtering and trimming of long read sequencing data
Filtering on quality and/or read length, and optional trimming after passing filters.Reads from stdin, writes to stdout. Intended to be used: directly after fastq extraction prior to mapping in a stream between extraction and mapping https://github.com/wdecoster/nanofilt2170 days ago
LSC :a long read error correction tool
...n Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong Improving PacBio Long Read Accuracy by Short Read Alignment [Manuscript] PLoS ONE 2012. 7(10): e46679....2167 days ago
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