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.2302 days ago
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.2294 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to j...inders from an adequate scaffolding evaluation are genome repeats. The previous standard for evaluation (Hunt et al., Genome...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 evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome...2272 days ago
SciLifeLab tutorial for bioinformatics analysis !
SciLifeLab is a national center for molecular biosciences with focus on health and envi...- Uppsala2018 February - Uppsala Introduction to Genome Annotation 2015 April - Upps...ala2017 April - Uppsala2018 May - Uppsala De Novo Genome...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 or scaffolds by reassembling them with help provided by a reference genome of a closely related organism...eads_1.fa --read2 reads_2.fa --contig contigs.fa --genome...2266 days ago
2265 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generatio...(both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BW...index that represents a population of human genomes...2246 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction fo...iction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic...all evidence for genes, from expressed sequences, genome...2246 days ago