2325 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/con...2313 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, including con...905 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 Alignment (WGA), and synteny). One is...904 days ago
Carefully opt for human reference genome
Heng Li posted several issues with the human reference genomes given in these resources and...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...17/11/13/which-human-reference-genome-to-use1593 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
REGEN infers evolutionary events, including gene creation and deletion and replicon...ncept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently relate...2307 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS, an application that utilizes the barc...inked 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 assembly drafts....2306 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to furt...that it can utilize multiple complete genomes of related organisms as refe...der and orient the contigs of a draft genome. In practical usage, our Mult...taset composed of several prokaryotic genomes and also compared its accura...2306 days ago
Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based on a fas...this is the first method to detect breakpoint reads without using a reference genome. https://github.com/ewijaya/...2305 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.2300 days ago