Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single referenc...hat it can utilize multiple complete genomes of related organisms as refe...er and orient the contigs of a draft genome. In practical usage, our Mult...aset composed of several prokaryotic genomes and a...2315 days ago
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. http...2313 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.2308 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.2300 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 Biolog...2300 days ago
2278 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 alignm...2278 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 Assemb...2273 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...2273 days ago
2271 days ago