GMOL: An Interactive Tool for 3D Genome Structure Visualization
GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.2296 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in b...hinders from an adequate scaffolding evaluation are genome repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not t...2296 days ago
2274 days ago
G-compass: a comparative genome browser
G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolution...enomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher co...2274 days ago
SciLifeLab tutorial for bioinformatics analysis !
...r - Lund2017 November - Uppsala2018 February - Uppsala Introduction to Genome Annotation 2015 April - Uppsala2016 April - Uppsala2017 April - Uppsala2018 May - Uppsala De Novo Genome Assembly 2016 November - Upp...2269 days ago
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
...igs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism...AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow dista...2269 days ago
2267 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
...sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BW...g one global GFM index that represents a population of human genomes, HISAT2 uses a large set of...2248 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Co...ion, and more recent gene assembly (de-novo and genome-assisted) methods. The basic...l evidence for genes, from expressed sequences, genome assembly sequences, related s...2248 days ago
Metassembler: merging and optimizing de novo genome assemblies
Metassembler combines multiple whole genome de novo assemblies into a combined cons...e best segments of the individual assemblies. Genome assembly projects typically r...algorithm that merges multiple assemblies of a genome into a single superior sequen...2248 days ago