HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution" Preprint: http://biorxiv.org/content/early/2016/08/01/062117 Paper: http://genome.cshlp.o...2337 days ago
GenomeTools: The versatile open source genome analysis software
The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a...sp;gt. It is based on a C library named “libgenometools&rd...2337 days ago
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 scaffo...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, in...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 Alignme...908 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-use1597 days ago
REGEN: Ancestral Genome Reconstruction for Bacteria
REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The recon...ept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that a...2311 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 assembl...2310 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 and al...2310 days ago