Technology dictates algorithms: recent developments in read alignment
Aligning sequencing reads onto a reference is an essential step of the majority of genomic
analysis pipelines. Computational algorithms for read alignment have evolved in …
analysis pipelines. Computational algorithms for read alignment have evolved in …
[HTML][HTML] Advances in optical mapping for genomic research
Recent advances in optical mapping have allowed the construction of improved genome
assemblies with greater contiguity. Optical mapping also enables genome comparison and …
assemblies with greater contiguity. Optical mapping also enables genome comparison and …
The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000
Hi-C contact maps are valuable for genome assembly (;;). Recently, we developed Juicebox,
a system for the visual exploration of Hi-C data, and 3D-DNA, an automated pipeline for …
a system for the visual exploration of Hi-C data, and 3D-DNA, an automated pipeline for …
Succinct de Bruijn graphs
A Bowe, T Onodera, K Sadakane, T Shibuya - International workshop on …, 2012 - Springer
We propose a new succinct de Bruijn graph representation. If the de Bruijn graph of k-mers
in a DNA sequence of length N has m edges, it can be represented in 4 m+ o (m) bits. This is …
in a DNA sequence of length N has m edges, it can be represented in 4 m+ o (m) bits. This is …
Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods
Background Recent advances in genomics indicate functional significance of a majority of
genome sequences and their long range interactions. As a detailed examination of genome …
genome sequences and their long range interactions. As a detailed examination of genome …
Succinct colored de Bruijn graphs
Abstract Motivation In 2012, Iqbal et al. introduced the colored de Bruijn graph, a variant of
the classic de Bruijn graph, which is aimed at 'detecting and genotyping simple and complex …
the classic de Bruijn graph, which is aimed at 'detecting and genotyping simple and complex …
Next generation sequencing of actinobacteria for the discovery of novel natural products
JP Gomez-Escribano, S Alt, MJ Bibb - Marine drugs, 2016 - mdpi.com
Like many fields of the biosciences, actinomycete natural products research has been
revolutionised by next-generation DNA sequencing (NGS). Hundreds of new genome …
revolutionised by next-generation DNA sequencing (NGS). Hundreds of new genome …
Current challenges and solutions of de novo assembly
Background Next‐generation sequencing (NGS) technologies have fostered an
unprecedented proliferation of high‐throughput sequencing projects and a concomitant …
unprecedented proliferation of high‐throughput sequencing projects and a concomitant …
[HTML][HTML] GAEP: a comprehensive genome assembly evaluating pipeline
Y Zhang, HW Lu, J Ruan - Journal of Genetics and Genomics, 2023 - Elsevier
With the rapid development of sequencing technologies, especially the maturity of third-
generation sequencing technologies, there has been a significant increase in the number …
generation sequencing technologies, there has been a significant increase in the number …
LRScaf: improving draft genomes using long noisy reads
Background The advent of third-generation sequencing (TGS) technologies opens the door
to improve genome assembly. Long reads are promising for enhancing the quality of …
to improve genome assembly. Long reads are promising for enhancing the quality of …