[HTML][HTML] Assembly algorithms for next-generation sequencing data
The emergence of next-generation sequencing platforms led to resurgence of research in
whole-genome shotgun assembly algorithms and software. DNA sequencing data from the …
whole-genome shotgun assembly algorithms and software. DNA sequencing data from the …
[HTML][HTML] One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
S Koren, AM Phillippy - Current opinion in microbiology, 2015 - Elsevier
… Author links open overlay panel Sergey Koren , Adam M Phillippy … As introduced by Koren
et al. [34 •• ], long-read correction involves mapping multiple reads to a single long read to …
et al. [34 •• ], long-read correction involves mapping multiple reads to a single long read to …
The muon Smasher's guide
…, IG Garcia, S Homiller, S Koren… - Reports on Progress …, 2022 - iopscience.iop.org
We lay out a comprehensive physics case for a future high-energy muon collider, exploring
a range of collision energies (from 1 to 100 TeV) and luminosities. We highlight the …
a range of collision energies (from 1 to 100 TeV) and luminosities. We highlight the …
The complete sequence of a human genome
Since its initial release in 2000, the human reference genome has covered only the
euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. …
euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. …
[HTML][HTML] Towards complete and error-free genome assemblies of all vertebrate species
High-quality and complete reference genome assemblies are fundamental for the application
of genomics to biology, disease, and biodiversity conservation. However, such assemblies …
of genomics to biology, disease, and biodiversity conservation. However, such assemblies …
[HTML][HTML] Nanopore sequencing and assembly of a human genome with ultra-long reads
We report the sequencing and assembly of a reference genome for the human GM12878
Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. …
Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. …
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
… a set Γ of s hash functions is defined for a sketch S of size s. Each sketch entry S i is defined
as … The resulting set of s minimum-valued k-mers, or min-mers, comprise the sketch. Given a …
as … The resulting set of s minimum-valued k-mers, or min-mers, comprise the sketch. Given a …
[HTML][HTML] A draft human pangenome reference
Here the Human Pangenome Reference Consortium presents a first draft of the human
pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of …
pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of …
[HTML][HTML] Mash: fast genome and metagenome distance estimation using MinHash
… MinHash sketches S(A) and S(B) of size s = 5 are shown for A and B, comprising the five …
S(A) and S(B) to recover the five smallest hash values overall for A∪B (crossed circles) yields S…
S(A) and S(B) to recover the five smallest hash values overall for A∪B (crossed circles) yields S…
[HTML][HTML] Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
… In the following sections, we describe how Merqury’s statistics and plots can be used to … We
note that Merqury’s methods are general and would be compatible with any reasonable high-…
note that Merqury’s methods are general and would be compatible with any reasonable high-…