P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
P_RNA_scaffolder, a fast and accurate tool using paired-end RNA-sequencing reads to scaffold genomes. This too...ures of both protein-coding genes and circular RNAs were almost completely recov...especially for long proteins and long circular RNAs.2169 days ago
2197 days ago
Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Ci...es using long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 1...2197 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compa...of each such structural feature. The bpRNA code is written in perl and r...lable at http://github.com/hendrixlab/bpRNA.2189 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
git clone https://github.com/lh3/minimap2 cd minimap2 && make # long sequen...omic paired-end reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam #...-uf ref.fa reads.fa > aln.sam # Nanopore Direct RNA-seq...2161 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable m...e feature labels in maps can be hyperlinked to external resources, allowing CGView m...t types, see the CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.ht...2160 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasible to study e...transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq...2148 days ago
2148 days ago
RNA-seq Analysis Workshop Course Materials
RNAseq can be roughly divided into two "types": Reference genome-base...nome exists for a species for which an RNAseq experiment is performed. I...using de novo approaches. This type of RNAseq is as much of an art as we...on the Reference genome-based type of RNA seq...2148 days ago
REVIGO: Reduced Visualize gene ontology
REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based...2120 days ago