DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
...for bench-marking. We further demonstrate that while existing tools are based on data generated from a specific sequencing technology, the models proposed in DAVI are generic and can b...1136 days ago
CISA: Contig Integrator for Sequence Assembly
A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optim...2688 days ago
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LIBSVM -- A Library for Support Vector Machines
...SVR) and distribution estimation (one-class SVM). It supports multi-class classification. Since version 2.8, it implements an SMO-type algorithm proposed in this paper:R.-E. Fan, P.-H...2458 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
...shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data. The initial approaches to assembling HP genomes were proposed in the pre-NGS era and are no...2317 days ago
RGFA: powerful and convenient handling of assembly graphs
RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the...1557 days ago
Reference-free prediction of rearrangement breakpoint reads
...t finds ∼88% of the breakpoints correctly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion t...2240 days ago
MIX: Combining multiple assemblies from NGS data
...e draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension...2179 days ago
LoRMA: A tool for correcting sequencing errors in long reads
...corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments, the proposed method is the most accurate o...2057 days ago