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 con...2235 days ago
NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
...apper designed to sensitively align PacBilo or Oxford Nanopore to...gned to quickly and correctly align the reads, including those sp...then a banded Smith-Waterman alignment algorithm to compute the...nd split reads that cannot be aligned linearly, enabling ngmlr to...2200 days ago
D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
...e dot plot to improve the visualisation. We use minimap version 2 to align the two genomes. Then, the PA...d3.js library. D-Genies also allows to display dot plots from other aligners by uploading their PAF or...2153 days ago
2150 days ago
LAMSA: fast split read alignment with long approximate matches
...pproximate Matches-based Split Aligner) is a novel split alignment approach with faster spee...V events. It is well-suited to align long reads (over thousands of...long fragments and co-linearly align them to solve the small varia...the state-of-the-art long read aligners; mean-while, it also has g...2180 days ago
2172 days ago
GenomeMapper: Simultaneous alignment of short reads against multiple genomes
...omeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. It can be used to align against multiple genomes simu...2170 days ago
2051 days ago
2030 days ago
COSINE: non-seeding method for mapping long noisy sequences
Third generation sequencing (TGS) are highly promising technologies but the long and noisy reads from TGS are difficult to align using existing algorithms. Here, we present COSINE, a conceptually new method designed specifically for aligning long reads contaminated by a high level of errors.2016 days ago