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.2293 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...2293 days ago
2272 days ago
G-compass: a comparative genome browser
G-compass (http://www.h-invitational.jp/g-compass/) is a comparative genome browser. It visualizes evolut...en human and other 12 vertebrates based on original genome alignments pursuing higher co...2272 days ago
SciLifeLab tutorial for bioinformatics analysis !
SciLifeLab is a national center for molecular biosciences...r - Uppsala2018 February - Uppsala Introduction to Genome Annotation 2015 April - Upps...sala2017 April - Uppsala2018 May - Uppsala De Novo Genome Assembly 2016 November - Upp...2267 days ago
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
AlignGraph is a software that extends and joins contigs o...reassembling them with help provided by a reference genome of a closely related organism...reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --distanceLow dista...2266 days ago
2265 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
...h DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BW...x that represents a population of human genomes, HISAT2 uses a large set of...GFM indexes that collectively cover the whole genome (each index representin...2246 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...2246 days ago
Metassembler: merging and optimizing de novo genome assemblies
Metassembler combines multiple whole genome de novo assemblies into a combined consensus...best segments of the individual assemblies. Genome assembly projects typically r...lgorithm that merges multiple assemblies of a genome into a single superior sequen...2246 days ago