scholarly journals Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing

2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Atul Sharma ◽  
Pranjal Jain ◽  
Ashraf Mahgoub ◽  
Zihan Zhou ◽  
Kanak Mahadik ◽  
...  
Keyword(s):  
Error Correction ◽  
Reference Genome ◽  
De Novo ◽  
Language Model ◽  
Assembly Quality ◽  
Sequencing Technologies ◽  
Before And After ◽  
Long Read ◽  
The One ◽  
After Error

Abstract Background Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parameters (e.g., k-mer size) are both tool- and dataset-dependent. Moreover, evaluating the performance (i.e., Alignment-rate or Gain) of a given tool usually relies on a reference genome, but quality reference genomes are not always available. We introduce Lerna for the automated configuration of k-mer-based EC tools. Lerna first creates a language model (LM) of the uncorrected genomic reads, and then, based on this LM, calculates a metric called the perplexity metric to evaluate the corrected reads for different parameter choices. Next, it finds the one that produces the highest alignment rate without using a reference genome. The fundamental intuition of our approach is that the perplexity metric is inversely correlated with the quality of the assembly after error correction. Therefore, Lerna leverages the perplexity metric for automated tuning of k-mer sizes without needing a reference genome. Results First, we show that the best k-mer value can vary for different datasets, even for the same EC tool. This motivates our design that automates k-mer size selection without using a reference genome. Second, we show the gains of our LM using its component attention-based transformers. We show the model’s estimation of the perplexity metric before and after error correction. The lower the perplexity after correction, the better the k-mer size. We also show that the alignment rate and assembly quality computed for the corrected reads are strongly negatively correlated with the perplexity, enabling the automated selection of k-mer values for better error correction, and hence, improved assembly quality. We validate our approach on both short and long reads. Additionally, we show that our attention-based models have significant runtime improvement for the entire pipeline—18$$\times$$ × faster than previous works, due to parallelizing the attention mechanism and the use of JIT compilation for GPU inferencing. Conclusion Lerna improves de novo genome assembly by optimizing EC tools. Our code is made available in a public repository at: https://github.com/icanforce/lerna-genomics.

scholarly journals De novo Nanopore read quality improvement using deep learning

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Nathan LaPierre ◽  
Rob Egan ◽  
Wei Wang ◽  
Zhong Wang
Keyword(s):  
Error Correction ◽  
Genome Assembly ◽  
Large Scale ◽  
De Novo ◽  
Error Rates ◽  
De Novo Genome Assembly ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Read Error Correction

Abstract Background Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area. Results Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent “scrubbing” (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments. Applying MiniScrub to real world control datasets under several different parameters, we show that it robustly improves read quality, and improves read error correction in the metagenome setting. Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer mis-assemblies and large indel errors. Conclusions MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub.

scholarly journals De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing

F1000Research ◽  
2018 ◽  
Vol 6 ◽  
pp. 618 ◽  
Author(s):  
Michael Liem ◽  
Hans J. Jansen ◽  
Ron P. Dirks ◽  
Christiaan V. Henkel ◽  
G. Paul H. van Heusden ◽  
...  
Keyword(s):  
De Novo ◽  
Sequence Data ◽  
New Technology ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Short Read ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Before And After ◽  
Long Read

Background: The introduction of the MinION sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing. Nanopore sequence data offers great potential for de novo assembly of complex genomes without using other technologies. Furthermore, Nanopore data combined with other sequencing technologies is highly useful for accurate annotation of all genes in the genome. In this manuscript we used nanopore sequencing as a tool to classify yeast strains. Methods: We compared various technical and software developments for the nanopore sequencing protocol, showing that the R9 chemistry is, as predicted, higher in quality than R7.3 chemistry. The R9 chemistry is an essential improvement for assembly of the extremely AT-rich mitochondrial genome. We double corrected assemblies from four different assemblers with PILON and assessed sequence correctness before and after PILON correction with a set of 290 Fungi genes using BUSCO. Results: In this study, we used this new technology to sequence and de novo assemble the genome of a recently isolated ethanologenic yeast strain, and compared the results with those obtained by classical Illumina short read sequencing. This strain was originally named Candida vartiovaarae (Torulopsis vartiovaarae) based on ribosomal RNA sequencing. We show that the assembly using nanopore data is much more contiguous than the assembly using short read data. We also compared various technical and software developments for the nanopore sequencing protocol, showing that nanopore-derived assemblies provide the highest contiguity. Conclusions: The mitochondrial and chromosomal genome sequences showed that our strain is clearly distinct from other yeast taxons and most closely related to published Cyberlindnera species. In conclusion, MinION-mediated long read sequencing can be used for high quality de novo assembly of new eukaryotic microbial genomes.

scholarly journals RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Krisztian Buza ◽  
Bartek Wilczynski ◽  
Norbert Dojer
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Real Data ◽  
Reference Sequence ◽  
Individual Genome ◽  
Single Experiment ◽  
Sequencing Technologies ◽  
Sequencing Cost ◽  
The Individual ◽  
Assembly Software

Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used.Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge.Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.

scholarly journals Mapping and phasing of structural variation in patient genomes using nanopore sequencing

2017 ◽  
Author(s):  
Mircea Cretu Stancu ◽  
Markus J. van Roosmalen ◽  
Ivo Renkens ◽  
Marleen Nieboer ◽  
Sjors Middelkamp ◽  
...  
Keyword(s):  
Single Molecule ◽  
De Novo ◽  
Structural Variants ◽  
Human Genetic Disease ◽  
Structural Genomic ◽  
Short Read ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Long Read ◽  
Complex Structural

AbstractStructural genomic variants form a common type of genetic alteration underlying human genetic disease and phenotypic variation. Despite major improvements in genome sequencing technology and data analysis, the detection of structural variants still poses challenges, particularly when variants are of high complexity. Emerging long-read single-molecule sequencing technologies provide new opportunities for detection of structural variants. Here, we demonstrate sequencing of the genomes of two patients with congenital abnormalities using the ONT MinION at 11x and 16x mean coverage, respectively. We developed a bioinformatic pipeline - NanoSV - to efficiently map genomic structural variants (SVs) from the long-read data. We demonstrate that the nanopore data are superior to corresponding short-read data with regard to detection of de novo rearrangements originating from complex chromothripsis events in the patients. Additionally, genome-wide surveillance of SVs, revealed 3,253 (33%) novel variants that were missed in short-read data of the same sample, the majority of which are duplications < 200bp in size. Long sequencing reads enabled efficient phasing of genetic variations, allowing the construction of genome-wide maps of phased SVs and SNVs. We employed read-based phasing to show that all de novo chromothripsis breakpoints occurred on paternal chromosomes and we resolved the long-range structure of the chromothripsis. This work demonstrates the value of long-read sequencing for screening whole genomes of patients for complex structural variants.

scholarly journals Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

2015 ◽  
Author(s):  
Sara Goodwin ◽  
James Gurtowski ◽  
Scott Ethe-Sayers ◽  
Panchajanya Deshpande ◽  
Michael Schatz ◽  
...  
Keyword(s):  
Error Correction ◽  
De Novo Assembly ◽  
De Novo ◽  
Correction Algorithm ◽  
Membrane Pore ◽  
Complete Representation ◽  
Oxford Nanopore ◽  
Long Read ◽  
Error Correction Algorithm ◽  
Sequencing Instrument

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used for sequencing the S. cerevisiae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Nanocorr (https://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such high error rate (between ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq data and produce a de novo assembly that is highly contiguous and accurate: the contig N50 length is more than ten-times greater than an Illumina-only assembly (678kb versus 59.9kbp), and has greater than 99.88% consensus identity when compared to the reference. Furthermore, the assembly with the long nanopore reads presents a much more complete representation of the features of the genome and correctly assembles gene cassettes, rRNAs, transposable elements, and other genomic features that were almost entirely absent in the Illumina-only assembly.

scholarly journals De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Joseph R. Fauver ◽  
John Martin ◽  
Gary J. Weil ◽  
Makedonka Mitreva ◽  
Peter U. Fischer
Keyword(s):  
Single Molecule ◽  
New Technologies ◽  
Reference Genome ◽  
De Novo ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Brugia Malayi ◽  
Field Isolates ◽  
Sequencing Technologies ◽  
Long Reads

AbstractFilarial nematode infections cause a substantial global disease burden. Genomic studies of filarial worms can improve our understanding of their biology and epidemiology. However, genomic information from field isolates is limited and available reference genomes are often discontinuous. Single molecule sequencing technologies can reduce the cost of genome sequencing and long reads produced from these devices can improve the contiguity and completeness of genome assemblies. In addition, these new technologies can make generation and analysis of large numbers of field isolates feasible. In this study, we assessed the performance of the Oxford Nanopore Technologies MinION for sequencing and assembling the genome of Brugia malayi, a human parasite widely used in filariasis research. Using data from a single MinION flowcell, a 90.3 Mb nuclear genome was assembled into 202 contigs with an N50 of 2.4 Mb. This assembly covered 96.9% of the well-defined B. malayi reference genome with 99.2% identity. The complete mitochondrial genome was obtained with individual reads and the nearly complete genome of the endosymbiotic bacteria Wolbachia was assembled alongside the nuclear genome. Long-read data from the MinION produced an assembly that approached the quality of a well-established reference genome using comparably fewer resources.

scholarly journals Comparative Study of Heart Rate, Blood Pressure and Selective Attention of Subjects Before and After Music

2019 ◽  
Vol 4 (1) ◽  
pp. 625-628
Author(s):  
Nisha Ghimire ◽  
Renu Yadav ◽  
Soumitra Mukhopadhyay
Keyword(s):  
Blood Pressure ◽  
Heart Rate ◽  
Reaction Time ◽  
Comparative Study ◽  
Error Correction ◽  
Vital Signs ◽  
Stroop Test ◽  
Before And After ◽  
Paired T Test ◽  
After Error

Introduction: Studies have shown different views regarding the effect of music in vitals e.g Heart rate (HR), Blood pressure (BP) and atiention. The effect of preferred music with lyrics in vitals and reaction time in stroop test has not been performed in Nepalese students so, we conducted the study. Objective: To find out the change in HR, BP and reaction time in Stroop test before and after their preferred music with lyrics. Methodology Thirty male medical and paramedical students aged 25.27 ± 2.0 participated in study. The vital signs and reaction time in Stroop test before and after music was taken. Results Paired-t test was used to compare means before and after exposure to music. The means are expressed as Mean ± SD. Heart rate (HR) increased after exposure to music (66.33±9.51 Vs 67.2±8.44) (p<.05). The error in Stroop test was less after music (.66±.49 Vs.63±.66) (p<.05). The reaction time after error correction decreased post exposure to music (24.117±4.61Vs23.29±4.45) (p<.05). Conclusion The heart rate increased after exposure to music. The errors decreased after listening to music which also decreased reaction time.

scholarly journals Closing Human Reference Genome Gaps: Identifying and Characterizing Gap-Closing Sequences

2020 ◽  
Vol 10 (8) ◽  
pp. 2801-2809 ◽  
Author(s):  
Tingting Zhao ◽  
Zhongqu Duan ◽  
Georgi Z. Genchev ◽  
Hui Lu
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Sequence Length ◽  
Sequencing Data ◽  
Human Reference Genome ◽  
Satellite Sequences ◽  
Long Read ◽  
Data Gap ◽  
Simple Repeats ◽  
Gap Closing

Despite continuous updates of the human reference genome, there are still hundreds of unresolved gaps which account for about 5% of the total sequence length. Given the availability of whole genome de novo assemblies, especially those derived from long-read sequencing data, gap-closing sequences can be determined. By comparing 17 de novo long-read sequencing assemblies with the human reference genome, we identified a total of 1,125 gap-closing sequences for 132 (16.9% of 783) gaps and added up to 2.2 Mb novel sequences to the human reference genome. More than 90% of the non-redundant sequences could be verified by unmapped reads from the Simons Genome Diversity Project dataset. In addition, 15.6% of the non-reference sequences were found in at least one of four non-human primate genomes. We further demonstrated that the non-redundant sequences had high content of simple repeats and satellite sequences. Moreover, 43 (32.6%) of the 132 closed gaps were shown to be polymorphic; such sequences may play an important biological role and can be useful in the investigation of human genetic diversity.

scholarly journals LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences

2016 ◽  
Author(s):  
Eric Disdero ◽  
Jonathan Filée
Keyword(s):  
Transposable Elements ◽  
Reference Genome ◽  
Genomic Analysis ◽  
Bioinformatic Tools ◽  
Sequencing Technologies ◽  
Population Genomic ◽  
Long Read ◽  
Different Strains ◽  
Low Coverage ◽  
Ncbi Blast

AbstractMotivationPopulation genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when short read sequences technology is used.ResultsLoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against Drosophila melanogaster PacBio datasets, LoRTE appears to be a reliable and broadly applicable tools to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences.Availability and ImplementationLoRTE is available at http://www.egce.cnrs-gif.fr/?p=6422. It is written in Python 2.7 and only requires the NCBI BLAST + package. LoRTE can be used on standard computer with limited RAM resources and reasonable running time even with large [email protected]

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