2329 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 fo...virus, containing many annotation tracks and new features, including conservation...908 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)...907 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-use1596 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
REGEN infers evolutionary events, including gene creation and deletion and replicon...oncept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently relate...2310 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS, an application that utilizes the ba...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....2310 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
...based scaffolding tool CAR into a new one called Multi-CAR such tha...it can utilize multiple complete genomes of related organisms as refe...and orient the contigs of a draft genome. In practical usage, our Mult...t composed of several prokaryotic genomes and also compared its accura...2310 days ago
Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based on a fa..., this is the first method to detect breakpoint reads without using a reference genome. https://github.com/ewijaya/...2308 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.2303 days ago