Systematic benchmarking of omics computational tools

S Mangul, LS Martin, BL Hill, AKM Lam… - Nature …, 2019‏ - nature.com
Computational omics methods packaged as software have become essential to modern
biological research. The increasing dependence of scientists on these powerful software …

Unicycler: resolving bacterial genome assemblies from short and long sequencing reads

RR Wick, LM Judd, CL Gorrie… - PLoS computational …, 2017‏ - journals.plos.org
The Illumina DNA sequencing platform generates accurate but short reads, which can be
used to produce accurate but fragmented genome assemblies. Pacific Biosciences and …

A comprehensive review of scaffolding methods in genome assembly

J Luo, Y Wei, M Lyu, Z Wu, X Liu, H Luo… - Briefings in …, 2021‏ - academic.oup.com
In the field of genome assembly, scaffolding methods make it possible to obtain a more
complete and contiguous reference genome, which is the cornerstone of genomic research …

ALLMAPS: robust scaffold ordering based on multiple maps

H Tang, X Zhang, C Miao, J Zhang, R Ming… - Genome biology, 2015‏ - Springer
The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an
essential step during de novo genome assembly. Because this process utilizes various …

MeDuSa: a multi-draft based scaffolder

E Bosi, B Donati, M Galardini, S Brunetti… - …, 2015‏ - academic.oup.com
Motivation: Completing the genome sequence of an organism is an important task in
comparative, functional and structural genomics. However, this remains a challenging issue …

Towards a whole‐genome sequence for rye (Secale cereale L.)

E Bauer, T Schmutzer, I Barilar, M Mascher… - The Plant …, 2017‏ - Wiley Online Library
We report on a whole‐genome draft sequence of rye (Secale cereale L.). Rye is a diploid
Triticeae species closely related to wheat and barley, and an important crop for food and …

Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

AJ Page, N De Silva, M Hunt, MA Quail… - Microbial …, 2016‏ - microbiologyresearch.org
The rapidly reducing cost of bacterial genome sequencing has lead to its routine use in
large-scale microbial analysis. Though map** approaches can be used to find differences …

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

A Bissett, A Fitzgerald, T Meintjes, PM Mele, F Reith… - GigaScience, 2016‏ - Springer
Background Microbial inhabitants of soils are important to ecosystem and planetary
functions, yet there are large gaps in our knowledge of their diversity and ecology. The …

The carbon footprint of bioinformatics

J Grealey, L Lannelongue, WY Saw… - Molecular biology …, 2022‏ - academic.oup.com
Bioinformatic research relies on large-scale computational infrastructures which have a
nonzero carbon footprint but so far, no study has quantified the environmental costs of …

ARCS: scaffolding genome drafts with linked reads

S Yeo, L Coombe, RL Warren, J Chu, I Birol - Bioinformatics, 2018‏ - academic.oup.com
Motivation Sequencing of human genomes is now routine, and assembly of shotgun reads is
increasingly feasible. However, assemblies often fail to inform about chromosome-scale …