Bandage: interactive visualization of de novo genome assemblies
...isplayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibi...de novo assemblies that are not possible through investigation of contigs alone. Availability and impl...2339 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
...When COPE is applied to real reads for genome assembly, the resulting contigs are found to have fewer error...ve a 14-fold improvement in the N50 measurement when compared with the contigs produced using unconnected re...2337 days ago
MeDuSa: a multi-draft based scaffolder
...xploits information obtained from a set of (draft or closed) genomes from related organisms to determine the correct order and orientation of the contigs. MeDuSa formalises the scaffo...2267 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number of metrics, including: Overall assembly length Number of scaffolds/contigs Length of longest scaffold/contig...2253 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
...ne called Multi-CAR such that it can utilize multiple complete genomes of related organisms as references to more accurately order and orient the contigs of a draft genome. In practic...2246 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.2240 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
...roblem in bioinformatics. It refers to joining assembly contigs into chains (called scaffolds). The join between two contigs A and B is considered correct...valuation framework considers the optimal assignment of contigs in the output scaffolding to...2231 days ago
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
...ignGraph is a software that extends and joins contigs or scaffolds by reassembling...-read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa --genome genome.fa --dista...nceHigh distancehigh --extendedContig extendedContigs.fa --remainingContig remainin...2204 days ago
MIX: Combining multiple assemblies from NGS data
...contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing...2184 days ago
EAGLER: a scaffolding tool for long reads.
...s input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio...2157 days ago