2332 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number of metrics, including: Overa...se presentations is generated using javascript from a common (JSON) data structure, allowing toggling between al...2319 days ago
UCSC SARS-CoV-2 Genome Browser
The UCSC SARS-CoV-2 Genome Browser (https://genome.ucsc.edu/covid19.html) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features,...911 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Al...910 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and sug...ed as hg38/GRCh38 human reference genome. if you map reads to GRCh38...: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_0000.../2017/11/13/which-human-reference-genome-to...1599 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The recons...cept of neighboring gene pairs. REGEN was designed to be used with any set of genomes t...2313 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS, an application that utilizes the barcoding information contained in...nked reads to further organize draft genomes into highly contiguous assem...contiguity of an ABySS H.sapiensgenome assembly can be increased ove...connecting high-quality sequences in genome as...2313 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single referenc...hat it can utilize multiple complete genomes of related organisms as refe...er and orient the contigs of a draft genome. In practical usage, our Mult...aset composed of several prokaryotic genomes a...2313 days ago
Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-al...this is the first method to detect breakpoint reads without using a reference genome....2311 days ago
SCUBAT: Scaffolding Contigs Using Blat And Transcripts
SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.2306 days ago