2330 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...2317 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...909 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...908 days ago
Carefully opt for human reference genome
...l issues with the human reference genomes given in these resources and...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-use1597 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
...um likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently relate...2311 days ago
ARCS: scaffolding genome drafts with linked reads
...ined in linked reads to further organize draft genomes into highly contiguous assem...w how the contiguity of an ABySS H.sapiensgenome assembly can be increased ove...data for connecting high-quality sequences in genome assembly drafts....2311 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
...CAR such that it can utilize multiple complete genomes of related organisms as refe...rately order and orient the contigs of a draft genome. In practical usage, our Mult...a real dataset composed of several prokaryotic genomes and also compared its accura...2311 days ago
Reference-free prediction of rearrangement breakpoint reads
...ches, and yet produces fewer false-positive reads. To our knowledge, this is the first method to detect breakpoint reads without using a reference genome. https://github.com/ewijaya/...2309 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.2304 days ago