Reference-free prediction of rearrangement breakpoint reads
lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-a...his is the first method to detect breakpoint reads without using a reference genome. https...2309 days ago
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.2304 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.2295 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to...nders from an adequate scaffolding evaluation are genome repeats. The previous standard for evaluation (Hunt et al., Genome Biology...2295 days ago
2273 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 alignme...2273 days ago
SciLifeLab tutorial for bioinformatics analysis !
SciLifeLab is a national center for molecular biosciences with focus on health and env...- Uppsala2018 February - Uppsala Introduction to Genome Annotation 2015 April - Upps...la2017 April - Uppsala2018 May - Uppsala De Novo Genome Assembl...2269 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...ads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome....2268 days ago
2267 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-generati...both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BW...ndex that represents a population of human genomes, HISAT...2248 days ago