scholarly journals GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads

2017 ◽  
Author(s):  
Chong Chu ◽  
Xin Li ◽  
Yufeng Wu
Keyword(s):  
Sequence Data ◽  
Bacterial Genome ◽  
Software Tool ◽  
Sea Bass ◽  
Short Sequence ◽  
Asian Sea Bass ◽  
Long Reads ◽  
Local Assembly ◽  
Genomic Repeats ◽  
Gap Closing

AbstractBackgroundClosing gaps in draft genomes is an important post processing step in genome assembly. It leads to more complete genomes, which benefits downstream genome analysis such as annotation and genotyping. Several tools have been developed for gap closing. However, these tools don’t fully utilize the information contained in the sequence data. For example, while it is known that many gaps are caused by genomic repeats, existing tools often ignore many sequence reads that originate from a repeat-related gap.ResultsIn this paper, we propose a new approach called GAPPadder for gap closing. The main advantage of GAPPadder is that it uses more information in sequence data for gap closing. In particular, GAPPadder finds and uses reads that originate from repeate-related gaps. We show that these repeat-associated reads are useful for gap closing, even though they are ignored by all existing tools. Other main features of GAPPadder include utilizing the information in sequence reads with different insert sizes and performing two-stage local assembly of gap sequences. We compare GAPPadder with GapCloser, GapFiller and Sealer on one bacterial genome, human chromosome 14 and the human whole genome with paired-end and mate-paired reads with both short and long insert sizes. Empirical results show that GAPPadder can close more gaps than these existing tools. Besides closing gaps on draft genomes assembled only from short sequence reads, GAPPadder can also be used to close gaps for draft genomes assembled with long reads. We show GAPPadder can close gaps on the bed bug genome and the Asian sea bass genome that are assembled partially and fully with long reads respectively. We also show GAPPadder is efficient in both time and memory usage. The software tool, GAPPadder, is available for download at https://github.com/Reedwarbler/GAPPadder.

scholarly journals TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads

GigaScience ◽  
2020 ◽  
Vol 9 (9) ◽  
Author(s):  
Mengyang Xu ◽  
Lidong Guo ◽  
Shengqiang Gu ◽  
Ou Wang ◽  
Rui Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Sequence Data ◽  
Software Tool ◽  
Fold Increase ◽  
Substantial Improvement ◽  
Large Genome ◽  
Long Reads ◽  
Close Sequence ◽  
Genome Assemblies ◽  
Large Genomes

Abstract Background Analyses that use genome assemblies are critically affected by the contiguity, completeness, and accuracy of those assemblies. In recent years single-molecule sequencing techniques generating long-read information have become available and enabled substantial improvement in contig length and genome completeness, especially for large genomes (>100 Mb), although bioinformatic tools for these applications are still limited. Findings We developed a software tool to close sequence gaps in genome assemblies, TGS-GapCloser, that uses low-depth (∼10×) long single-molecule reads. The algorithm extracts reads that bridge gap regions between 2 contigs within a scaffold, error corrects only the candidate reads, and assigns the best sequence data to each gap. As a demonstration, we used TGS-GapCloser to improve the scaftig NG50 value of 3 human genome assemblies by 24-fold on average with only ∼10× coverage of Oxford Nanopore or Pacific Biosciences reads, covering with sequence data up to 94.8% gaps with 97.7% positive predictive value. These improved assemblies achieve 99.998% (Q46) single-base accuracy with final inserted sequences having 99.97% (Q35) accuracy, despite the high raw error rate of single-molecule reads, enabling high-quality downstream analyses, including up to a 31-fold increase in the scaftig NGA50 and up to 13.1% more complete BUSCO genes. Additionally, we show that even in ultra-large genome assemblies, such as the ginkgo (∼12 Gb), TGS-GapCloser can cover 71.6% of gaps with sequence data. Conclusions TGS-GapCloser can close gaps in large genome assemblies using raw long reads quickly and cost-effectively. The final assemblies generated by TGS-GapCloser have improved contiguity and completeness while maintaining high accuracy. The software is available at https://github.com/BGI-Qingdao/TGS-GapCloser.

scholarly journals TGS-GapCloser: fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads

2019 ◽  
Author(s):  
Mengyang Xu ◽  
Lidong Guo ◽  
Shengqiang Gu ◽  
Ou Wang ◽  
Rui Zhang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Annotation ◽  
Variant Calling ◽  
Software Tool ◽  
Error Rates ◽  
Third Generation ◽  
Large Genome ◽  
Long Reads ◽  
Genome Assemblies ◽  
Gap Closing

AbstractThe completeness and accuracy of genome assemblies determine the quality of subsequent bioinformatics analysis. Despite benefiting from the medium/long-range information of third-generation sequencing techniques, current gap-closing tools to enhance assemblies suffer multi-alignments and high error rates, resulting in huge time and money costs.We developed a software tool, TGS-GapCloser that uses the low depth (>=10X) single molecule sequencing long reads without any error correction to close gaps. The algorithm distinguishes gap regions from the alignments of long reads against original scaffolds, corrects only the candidate regions, and assigns the best sequences to each gap. We demonstrate that TGS-GapCloser improves the contig N50 value of draft assembly by 25-fold on average, updating above 90% gaps with 93.96% positive predictive value. Despite of high error rate of raw long reads, improved assemblies archive Q50 (99.999%) single-base accuracy with only 11.8% decrement to inputs. Besides it could complete more gaps, and is also ∼29-fold faster than mainstream gap-closing tools. BUSCO analysis revealed that 3.4%-13.1% more expected genes were complete. TGS-GapCloser also shows its power to fill gaps for ultra large genome assembly of ginkgo (∼12Gb) with 71.6% of gaps closed. The validation of inserted or merged gap sequences was conducted with NGS reads and reference genomes, respectively. The updated genome assemblies may promote the gene annotation, structure variant calling and thus improving the downstream analysis of ontogeny, phylogeny, and evolution.

scholarly journals Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Vahid Akbari ◽  
Jean-Michel Garant ◽  
Kieran O’Neill ◽  
Pawan Pandoh ◽  
Richard Moore ◽  
...  
Keyword(s):  
Sequence Data ◽  
Software Tool ◽  
Nanopore Sequencing ◽  
Post Process ◽  
Genome Wide ◽  
Long Reads ◽  
Improve Accuracy ◽  
Allele Specific ◽  
Allele Specific Methylation ◽  
Low Coverage

AbstractThe ability of nanopore sequencing to simultaneously detect modified nucleotides while producing long reads makes it ideal for detecting and phasing allele-specific methylation. However, there is currently no complete software for detecting SNPs, phasing haplotypes, and mapping methylation to these from nanopore sequence data. Here, we present NanoMethPhase, a software tool to phase 5-methylcytosine from nanopore sequencing. We also present SNVoter, which can post-process nanopore SNV calls to improve accuracy in low coverage regions. Together, these tools can accurately detect allele-specific methylation genome-wide using nanopore sequence data with low coverage of about ten-fold redundancy.

Physical and chemical characteristics of Asian sea bass bio‐calcium powders as affected by ultrasonication treatment and drying method

2021 ◽  
Vol 45 (4) ◽  
Author(s):  
Ima Wijayanti ◽  
Pornsatit Sookchoo ◽  
Thummanoon Prodpran ◽  
Chitradurga O. Mohan ◽  
Rotimi E. Aluko ◽  
...  
Keyword(s):  
Sea Bass ◽  
Chemical Characteristics ◽  
Drying Method ◽  
Physical And Chemical Characteristics ◽  
Asian Sea Bass ◽  
Physical And Chemical

β-Defensin from the Asian Sea Bass, Lates calcarifer: Molecular Prediction and Phylogenetic Analysis

2021 ◽  
Author(s):  
Athira Raveendran ◽  
Dhanya Lenin K. L. ◽  
Anju M.V. ◽  
Neelima S. ◽  
Anooja V.V. ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sea Bass ◽  
Lates Calcarifer ◽  
Asian Sea Bass

scholarly journals A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

2021 ◽  
Author(s):  
Guangtu Gao ◽  
Susana Magadan ◽  
Geoffrey C Waldbieser ◽  
Ramey C Youngblood ◽  
Paul A Wheeler ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Chromosome Number ◽  
Genome Assembly ◽  
De Novo Assembly ◽  
De Novo ◽  
Sequence Data ◽  
Structural Variations ◽  
High Coverage ◽  
Haploid Chromosome Number ◽  
Long Reads

Abstract Currently, there is still a need to improve the contiguity of the rainbow trout reference genome and to use multiple genetic backgrounds that will represent the genetic diversity of this species. The Arlee doubled haploid line was originated from a domesticated hatchery strain that was originally collected from the northern California coast. The Canu pipeline was used to generate the Arlee line genome de-novo assembly from high coverage PacBio long-reads sequence data. The assembly was further improved with Bionano optical maps and Hi-C proximity ligation sequence data to generate 32 major scaffolds corresponding to the karyotype of the Arlee line (2 N = 64). It is composed of 938 scaffolds with N50 of 39.16 Mb and a total length of 2.33 Gb, of which ∼95% was in 32 chromosome sequences with only 438 gaps between contigs and scaffolds. In rainbow trout the haploid chromosome number can vary from 29 to 32. In the Arlee karyotype the haploid chromosome number is 32 because chromosomes Omy04, 14 and 25 are divided into six acrocentric chromosomes. Additional structural variations that were identified in the Arlee genome included the major inversions on chromosomes Omy05 and Omy20 and additional 15 smaller inversions that will require further validation. This is also the first rainbow trout genome assembly that includes a scaffold with the sex-determination gene (sdY) in the chromosome Y sequence. The utility of this genome assembly is demonstrated through the improved annotation of the duplicated genome loci that harbor the IGH genes on chromosomes Omy12 and Omy13.

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