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Systematic benchmarking of omics computational tools
Computational omics methods packaged as software have become essential to modern
biological research. The increasing dependence of scientists on these powerful software …
biological research. The increasing dependence of scientists on these powerful software …
Unicycler: resolving bacterial genome assemblies from short and long sequencing reads
The Illumina DNA sequencing platform generates accurate but short reads, which can be
used to produce accurate but fragmented genome assemblies. Pacific Biosciences and …
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 …
complete and contiguous reference genome, which is the cornerstone of genomic research …
ALLMAPS: robust scaffold ordering based on multiple maps
The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an
essential step during de novo genome assembly. Because this process utilizes various …
essential step during de novo genome assembly. Because this process utilizes various …
MeDuSa: a multi-draft based scaffolder
Motivation: Completing the genome sequence of an organism is an important task in
comparative, functional and structural genomics. However, this remains a challenging issue …
comparative, functional and structural genomics. However, this remains a challenging issue …
Towards a whole‐genome sequence for rye (Secale cereale L.)
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 …
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
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 …
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
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 …
functions, yet there are large gaps in our knowledge of their diversity and ecology. The …
The carbon footprint of bioinformatics
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 …
nonzero carbon footprint but so far, no study has quantified the environmental costs of …
ARCS: scaffolding genome drafts with linked reads
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 …
increasingly feasible. However, assemblies often fail to inform about chromosome-scale …