MUMmer4: A fast and versatile genome alignment system
MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure...bsp;program in MUMmer4 is easily able to handle alignments of large genomes; ...2346 days ago
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....2342 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&r...2342 days ago
2334 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 scaff...2321 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, i...913 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 Alignm...912 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-use1601 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...2315 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 assemb...2315 days ago