Opera: An optimal genome scaffolding program
...for the assembly of large and complex genomes.Song Gao, Denis Bertrand, Burton K. H. Chia and Niranjan Nagarajan. OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryo...2348 days ago
MeDuSa: a multi-draft based scaffolder
MeDuSa (Multi-Draft based Scaffolder), an algorithm for genome scaffolding. MeDuSa exploits information obtain...correct order and orientation of the contigs. MeDuSa formalises the scaffolding problem by means of a combina...2269 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS, an application that utilizes the barcoding information contained in linked reads to further organize draft genomes into highly contiguous assemblies. We show how th...2249 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
...simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one calle...ompared its accuracy performance with other multiple reference-based scaffolding tools Ragout and MeDuSa. ...2249 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.2242 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinform...rue distance on the reference The problem of scaffolding validation is also a challeng...the main issues which hinders from an adequate scaffolding evaluation are genome repeats...2234 days ago
EAGLER: a scaffolding tool for long reads.
EAGLER is a scaffolding tool for long reads. The scaffolder takes as input a draft genome created by any NGS assembler and a set of long reads. The long reads are used to exten...2159 days ago
P_RNA_scaffolder: a fast and accurate genome scaffolder using paired-end RNA-sequencing reads
...ads to scaffold genomes. This tool aims to improve the completeness of both protein-coding and non-coding genes. After this tool was applied to scaffolding human contigs, the structures...2151 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...SIS. Manuscript describing LACHESIS was published as: Burton JN#, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J#. Chromosome-scale scaffolding of de novo genome assemblies...2180 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...t;1 megabase. This software, fragScaff, leverages coincidences between the content of different pools as a source of contiguity information for scaffolding de novo genome assemblies. Fr...2180 days ago