2485 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...iniasm finishes the assembly, including reads overlapping, in ~10 minutes with 16 C...that minimap can be used as a read overlapper, even though it is probabl...sm && (cd miniasm && make) # Overlap minimap/minimap -Sw5 -L100 -...2345 days ago
2343 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
...ike other state-of-the-art assemblers, Ra does not have an error correction step. Instead, it relies on detecting overlaps using a very sensitive and specific overlapper ("graphmap -w owler", ...2315 days ago
HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution
...p.org/content/27/5/747.full An ipython notebook to reproduce results in the paper can be found in this repository. HINGE is an OLC(Overlap-Layout-Consensus) assembler....2273 days ago
2187 days ago
2155 days ago
minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences
...cx asm5 asm1.fa asm2.fa > aln.paf # intra-species asm-to-asm alignment ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf # PacBio read overlap ./minimap2 -x ava-ont reads....2140 days ago
BAUM – Improving Genome Assembly by Adaptive Unique Mapping and Local Overlap-Layout-Consensus
BAUM, breaks the whole genome into regions by adaptive unique mapping; then the local OLC is used to assemble each region in parallel. BAUM can: (1) perform reference-a...2014 days ago
GeneOverlap: An R package to test and visualize gene overlaps
Overlapping gene lists can reveal biological meanings and...experiments. Because of its activating role, if we overlap the genes that are bound by H...association. Similary, we can perform such kind of overlapping between the gene lists of...1950 days ago