lamassemble: Multiple Alignment and Consensus Sequence of Long Reads

2020 ◽  
pp. 135-145
Author(s):  
Martin C. Frith ◽  
Satomi Mitsuhashi ◽  
Kazutaka Katoh
Keyword(s):  
Consensus Sequence ◽  
Multiple Alignment ◽  
Long Reads

scholarly journals A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Eugenie C Yen ◽  
Shane A McCarthy ◽  
Juan A Galarza ◽  
Tomas N Generalovic ◽  
Sarah Pelan ◽  
...  
Keyword(s):  
Population Structure ◽  
Genome Assembly ◽  
De Novo ◽  
Consensus Sequence ◽  
Parental Origin ◽  
De Novo Genome Assembly ◽  
Geographic Population ◽  
Long Reads ◽  
Tiger Moth ◽  
Innovative Solution

ABSTRACT Background Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism. Findings We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity. Conclusions We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.

scholarly journals Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing

2019 ◽  
Author(s):  
Agnes Scheunert ◽  
Marco Dorfner ◽  
Thomas Lingl ◽  
Christoph Oberprieler
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Consensus Sequence ◽  
Suitable Alternative ◽  
Short Read ◽  
Chloroplast Genomes ◽  
Long Reads ◽  
Illumina Data

AbstractThe chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes. PacBio or Oxford Nanopore long reads are additionally employed in hybrid approaches to enable assembly across the highly similar inverted repeats of a chloroplast genome. Unlike for PacBio, plastome assemblies based solely on Nanopore reads are rarely found, due to their high error rate and non-random error profile. However, the actual quality decline connected to their use has never been quantified. Furthermore, no study has employed reference-based assembly using Nanopore reads, which is common with Illumina data. Using Leucanthemum Mill. as an example, we compared the sequence quality of seven plastome assemblies of the same species, using combinations of two sequencing platforms and three analysis pipelines. In addition, we assessed the factors which might influence Nanopore assembly quality during sequence generation and bioinformatic processing.The consensus sequence derived from de novo assembly of Nanopore data had a sequence identity of 99.59% compared to Illumina short-read de novo assembly. Most of the found errors comprise indels (81.5%), and a large majority of them is part of homopolymer regions. The quality of reference-based assembly is heavily dependent upon the choice of a close-enough reference. Using a reference with 0.83% sequence divergence from the studied species, mapping of Nanopore reads results in a consensus comparable to that from Nanopore de novo assembly, and of only slightly inferior quality compared to a reference-based assembly with Illumina data (0.49% and 0.26% divergence from Illumina de novo). For optimal assembly of Nanopore data, appropriate filtering of contaminants and chimeric sequences, as well as employing moderate read coverage, is essential.Based on these results, we conclude that Nanopore long reads are a suitable alternative to Illumina short reads in plastome phylogenomics. Only few errors remain in the finalized assembly, which can be easily masked in phylogenetic analyses without loss in analytical accuracy. The easily applicable and cost-effective technology might warrant more attention by researchers dealing with plant chloroplast genomes.

scholarly journals Chromosome-scale reference genome assembly of a diploid potato clone derived from an elite variety

2021 ◽  
Author(s):  
Ruth Freire ◽  
Marius Weisweiler ◽  
Ricardo Guerreiro ◽  
Nadia Baig ◽  
Bruno Hüttel ◽  
...  
Keyword(s):  
Reference Genome ◽  
Solanum Tuberosum L ◽  
Consensus Sequence ◽  
Sequence Divergence ◽  
Potato Genome ◽  
Proximity Ligation ◽  
Final Assembly ◽  
Diploid Clone ◽  
Long Reads ◽  
Genome Assemblies

Abstract Potato (Solanum tuberosum L.) is one of the most important crops with a world-wide production of 370 million metric tons. The objectives of this study were (i) to create a high quality consensus sequence across the two haplotypes of a diploid clone derived from a tetraploid elite variety and assess the sequence divergence from the available potato genome assemblies, as well as among the two haplotypes; (ii) to evaluate the new assembly’s usefulness for various genomic methods and (iii) to assess the performance of phasing in diploid and tetraploid clones, using linked read sequencing technology. We used PacBio long reads coupled with 10x Genomics reads and proximity-ligation scaffolding to create the dAg1_v1.0 reference genome sequence. With a final assembly size of 812 Mb, where 750 Mb are anchored to 12 chromosomes, our assembly is larger than other available potato reference sequences and high proportions of properly paired reads were observed for clones unrelated by pedigree to dAg1. Comparisons of the new dAg1_v1.0 sequence to other potato genome sequences point out the high divergence between the different potato varieties and illustrate the potential of using dAg1_v1.0 sequence in breeding applications.

scholarly journals A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning

2020 ◽  
Author(s):  
Eugenie C. Yen ◽  
Shane A. McCarthy ◽  
Juan A. Galarza ◽  
Tomas N. Generalovic ◽  
Sarah Pelan ◽  
...  
Keyword(s):  
Population Structure ◽  
Genome Assembly ◽  
De Novo ◽  
Consensus Sequence ◽  
Parental Origin ◽  
De Novo Genome Assembly ◽  
Geographic Population ◽  
Long Reads ◽  
Tiger Moth ◽  
Innovative Solution

ABSTRACTBackgroundDiploid genome assembly is typically impeded by heterozygosity, as it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an innovative solution which exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism.FindingsWe produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked-reads. Both assemblies are highly contiguous (mean scaffold N50: 8.2Mb) and complete (mean BUSCO completeness: 97.3%), with complete annotations and 31 chromosomes identified through karyotyping. We employed the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from five populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity.ConclusionsWe present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling highly heterozygous genomes. Using this assembly, we provide genomic insights into geographic population structure of Arctia plantaginis.

MASH: an interactive program for multiple alignment and consensus sequence construction for biological sequences

1991 ◽  
Vol 7 (2) ◽  
pp. 195-202
Author(s):  
C. Chappey ◽  
A. Danckaert ◽  
P. Dessen ◽  
S. Hazout
Keyword(s):  
Consensus Sequence ◽  
Multiple Alignment ◽  
Interactive Program ◽  
Biological Sequences

scholarly journals GPU accelerated partial order multiple sequence alignment for long reads self-correction

2020 ◽  
Author(s):  
Francesco Peverelli ◽  
Lorenzo Di Tucci ◽  
Marco D. Santambrogio ◽  
Nan Ding ◽  
Steven Hofmeyr ◽  
...  
Keyword(s):  
Error Correction ◽  
Partial Order ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Consensus Sequence ◽  
Pairwise Alignment ◽  
Multiple Sequence ◽  
Graph Alignment ◽  
Correction Process ◽  
Long Reads

AbstractAs third generation sequencing technologies become more reliable and widely used to solve several genome-related problems, self-correction of long reads is becoming the preferred method to reduce the error rate of Pacific Biosciences and Oxford Nanopore long reads, that is now around 10-12%. Several of these self-correction methods rely on some form of Multiple Sequence Alignment (MSA) to obtain a consensus sequence for the original reads. In particular, error-correction tools such as RACON and CONSENT use Partial Order (PO) graph alignment to accomplish this task. PO graph alignment, which is computationally more expensive than optimal global pairwise alignment between two sequences, needs to be performed several times for each read during the error correction process. GPUs have proven very effective in accelerating several compute-intensive tasks in different scientific fields. We harnessed the power of these architectures to accelerate the error correction process of existing self-correction tools, to improve the efficiency of this step of genome analysis.In this paper, we introduce a GPU-accelerated version of the PO alignment presented in the POA v2 software library, implemented on an NVIDIA Tesla V100 GPU. We obtain up to 6.5x speedup compared to 64 CPU threads run on two 2.3 GHz 16-core Intel Xeon Processors E5-2698 v3. In our implementation we focused on the alignment of smaller sequences, as the CONSENT segmentation strategy based on k-mer chaining provides an optimal opportunity to exploit the parallel-processing power of GPUs. To demonstrate this, we have integrated our kernel in the CONSENT software. This accelerated version of CONSENT provides a speedup for the whole error correction step that ranges from 1.95x to 8.5x depending on the input reads.

scholarly journals TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain

2019 ◽  
Vol 35 (14) ◽  
pp. i200-i207 ◽  
Author(s):  
Yan Gao ◽  
Bo Liu ◽  
Yadong Wang ◽  
Yi Xing
Keyword(s):  
Tandem Repeat ◽  
Rolling Circle Amplification ◽  
Consensus Sequence ◽  
Error Rates ◽  
Sequencing Error ◽  
Template Molecule ◽  
Long Reads ◽  
Pattern Size ◽  
Repeat Pattern ◽  
Repeat Detection

Abstract Motivation Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) sequencing technologies can produce long-reads up to tens of kilobases, but with high error rates. In order to reduce sequencing error, Rolling Circle Amplification (RCA) has been used to improve library preparation by amplifying circularized template molecules. Linear products of the RCA contain multiple tandem copies of the template molecule. By integrating additional in silico processing steps, these tandem sequences can be collapsed into a consensus sequence with a higher accuracy than the original raw reads. Existing pipelines using alignment-based methods to discover the tandem repeat patterns from the long-reads are either inefficient or lack sensitivity. Results We present a novel tandem repeat detection and consensus calling tool, TideHunter, to efficiently discover tandem repeat patterns and generate high-quality consensus sequences from amplified tandemly repeated long-read sequencing data. TideHunter works with noisy long-reads (PacBio and ONT) at error rates of up to 20% and does not have any limitation of the maximal repeat pattern size. We benchmarked TideHunter using simulated and real datasets with varying error rates and repeat pattern sizes. TideHunter is tens of times faster than state-of-the-art methods and has a higher sensitivity and accuracy. Availability and implementation TideHunter is written in C, it is open source and is available at https://github.com/yangao07/TideHunter

Plasmid Sequence Analysis from Long Reads v2

2021 ◽  
Author(s):  
David A Eccles
Keyword(s):  
Sequence Analysis ◽  
Plasmid Dna ◽  
De Novo ◽  
Consensus Sequence ◽  
Fasta File ◽  
High Quality ◽  
Plasmid Sequence ◽  
Long Reads ◽  
The Moment

This protocol demonstrates how to assemble reads from plasmid DNA, and generate a circularised and non-repetitive consensus sequence At the moment, this protocol uses Canu to de-novo assemble high-quality single-cut reads. Input(s): demultiplexed fastq files (see protocol Demultiplexing Nanopore reads with LAST). I've noticed that the default demultiplexing carried out by Guppy (at least up to v4.2.2, as used in the first version of this protocol) has issues with chimeric reads, which can affect assembly. Output(s): Consensus sequence per barcode as a fasta file

scholarly journals DENTIST – using long reads to close assembly gaps at high accuracy

2021 ◽  
Author(s):  
Arne Ludwig ◽  
Martin Pippel ◽  
Gene Myers ◽  
Michael Hiller
Keyword(s):  
Consensus Sequence ◽  
High Accuracy ◽  
Short Read ◽  
Application Range ◽  
Link Type ◽  
Long Reads ◽  
High Base ◽  
The Right ◽  
Genome Assemblies ◽  
The Given

AbstractLong sequencing reads allow increasing contiguity and completeness of fragmented, shortread based genome assemblies by closing assembly gaps, ideally at high accuracy. While several gap closing methods have been developed, these methods often close an assembly gap with sequence that does not accurately represent the true sequence.Here, we developed DENTIST, a sensitive, highly-accurate and automated pipeline method to close gaps in short read assemblies with long reads. DENTIST comprehensively determines repetitive assembly regions to identify reliable and unambiguous alignments of long reads to the right loci, integrates a consensus sequence computation step to obtain a high base accuracy for the inserted sequence, and validates the accuracy of closed gaps. Unlike previous benchmarks, we generated test assemblies that have gaps at the exact positions where real short-read assemblies have gaps. Generating such realistic benchmarks for Drosophila (134 Mb genome), Arabidopsis (119 Mb), hummingbird (1 Gb) and human (3 Gb) and using simulated or real PacBio reads, we show that DENTIST consistently achieves a substantially higher accuracy compared to previous methods, while having a similar sensitivity. As another distinguishing feature, DENTIST can accurately scaffold the given contigs with long reads in addition to closing gaps, extending its application range to contig-only assemblies.In summary, DENTIST provides an accurate approach to improve the contiguity and completeness of fragmented assemblies with long reads. DENTIST’s source code including a Snakemake workflow and Docker container is available at https://github.com/a-ludi/dentist. All test assemblies as a resource for future benchmarking are at https://bds.mpi-cbg.de/hillerlab/DENTIST/.

scholarly journals Efficient hybrid de novo assembly of human genomes with WENGAN

2020 ◽  
Author(s):  
Alex Di Genova ◽  
Elena Buena-Atienza ◽  
Stephan Ossowski ◽  
Marie-France Sagot
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Consensus Sequence ◽  
Computational Cost ◽  
Sequencing Data ◽  
Human Genomes ◽  
Long Reads ◽  
High Gene ◽  
Computational Resources ◽  
Genome Assemblies

AbstractGenerating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very high quality at low computational cost. We demonstrate de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel, Illumina and MGI technology. WENGAN implements efficient algorithms to improve assembly contiguity as well as consensus quality. The resulting genome assemblies have high contiguity (contig NG50: 17.24–80.64 Mb), few assembly errors (contig NGA50: 11.8–59.59 Mb), good consensus quality (QV: 27.84–42.88) and high gene completeness (BUSCO complete: 94.6–95.2%), while consuming low computational resources (CPU hours: 187–1,200). In particular, the WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64 Mb (NGA50: 59.59 Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50: 57.88 Mb).

Sign in / Sign up

Export Citation Format

Share Document