Results for "scaffolding"
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SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.Tags: SWALO, Scaffolding, assembly, likelihood, optimization
2140 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a close...Tags: RaGOO, Fast, Reference-Guided, Scaffolding, Genome, Assembly, Contigs
1839 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a close...Tags: RaGOO, Fast, Reference, Guided, Scaffolding, Genome, Assembly, Contigs, NGS
1646 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.An updated version called OPERA-LG has b...Tags: Opera, optimal, genome, scaffolding, program
2345 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 the contiguity of an ABySS H.sapiensgenome assembly can be increased over six-fold, using moderate coverage (25-fold) Chromi...Tags: ARCS, scaffolding, genome, drafts, linked, reads
2246 days ago
Multi-CAR: a tool of contig scaffolding using multiple references
we design a simple heuristic method to further revise our single reference-based scaffolding tool CAR into a new one 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...Tags: Multi-CAR, tool, contig, scaffolding, multiple, references
2246 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to joining assembly contigs into chains (called scaffolds). The join between two contigs A and B is considered correct if: Their relative orientation is correct Their relative order is correct The gap estimate...Tags: Repeat, aware, scaffolding, evaluation, framework, Igor, Mandric, repeat-aware
2231 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 extend the contigs present in the NGS draft and possibly join overlapping contigs. EAGLER supports both PacBio and Oxford Nano...Tags: EAGLER, scaffolding, tool, long, reads, genome, assembly
2156 days ago
