Genomes correction and assembling: present methods and tools

Wojcieszek, Michał; Pawełkowicz, Magdalena; Nowak, Robert; Przybecki, Zbigniew

doi:10.1117/12.2075624

Cited by 6 publications

(2 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although it seems simple at first glance, the metagenome assembly problem is actually quite complex. Among the several challenges this task arises, there are sequencing errors specific to each platform and the processing of the large volume of data produced by NGS platforms [8]. Moreover, the problem is further complicated by variations on the size of the genomes and also by the complexity, diversity and abundance of each organism present in a microbial community [9].…”

Section: Introductionmentioning

confidence: 99%

Improving Metagenomic Assemblies Through Data Partitioning: a GC content approach

Miranda

Batista

Silva

et al. 2018

Preprint

View full text Add to dashboard Cite

Assembling metagenomic data sequenced by NGS platforms poses significant computational challenges, especially due to large volumes of data, sequencing errors, and variations in size, complexity, diversity and abundance of organisms present in a given metagenome. To overcome these problems, this work proposes an open-source, bioinformatic tool called GCSplit, which partitions metagenomic sequences into subsets using a computationally inexpensive metric: the GC content. Experiments performed on real data show that preprocessing short reads with GCSplit prior to assembly reduces memory consumption and generates higher quality results, such as an increase in the N50 metric and the reduction in both the L50 value and the total number of contigs produced in the assembly. GCSplit is available at https://github.com/ mirand863/gcsplit.

show abstract

Section: Introductionmentioning

confidence: 99%

Improving Metagenomic Assemblies Through Data Partitioning: a GC content approach

Miranda

Batista

Silva

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…Next generation sequencing (NGS) platforms have reduced sequencing costs and increased the amount of data generated, resulting in a greater number of complete genomes for eukaryotes and prokaryotes, which are subsequently deposited in public databases [ 1 , 2 ].…”

Section: Introductionmentioning

confidence: 99%

GapBlaster—A Graphical Gap Filler for Prokaryote Genomes

et al. 2016

View full text Add to dashboard Cite

The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.

show abstract