New strategies to improve minimap2 alignment accuracy.
Ontology highlight
ABSTRACT: Summary
We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions up to 100 kb by default, addressing major weakness in minimap2 v2.18 or earlier.Availability and implementation
https://github.com/lh3/minimap2.
SUBMITTER: Li H
PROVIDER: S-EPMC8652018 | biostudies-literature | 2021 Dec
REPOSITORIES: biostudies-literature
Publications
New strategies to improve minimap2 alignment accuracy.
Bioinformatics (Oxford, England) 20211201 23
<h4>Summary</h4>We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions up to 100 kb by default, addressing major weakness in minimap2 v2.18 or earlier.<h4>Availability and implementation</h4>https://github.com/lh3/minimap2. ...[more]
Similar Datasets
Project description:Motivation:Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms. Results:Minimap2 is a general-purpose alignment program to map DNA or long mRNA sequences against a large reference database. It works with accurate short reads of ≥100 bp in length, ≥1 kb genomic reads at error rate ∼15%, full-length noisy Direct RNA or cDNA reads and assembly contigs or closely related full chromosomes of hundreds of megabases in length. Minimap2 does split-read alignment, employs concave gap cost for long insertions and deletions and introduces new heuristics to reduce spurious alignments. It is 3-4 times as fast as mainstream short-read mappers at comparable accuracy, and is ≥30 times faster than long-read genomic or cDNA mappers at higher accuracy, surpassing most aligners specialized in one type of alignment. Availability and implementation:https://github.com/lh3/minimap2. Supplementary information:Supplementary data are available at Bioinformatics online.
| S-EPMC6137996 | biostudies-literature
Project description:In the United States, colorectal cancer (CRC) is the second-leading cause of cancer-related deaths. The most effective strategy for prevention of CRC is to screen for and remove precancerous polyps. There are various ways to screen for CRC. In the United States, the most common method is colonoscopy. Polyps are classified primarily through pathology. Size is the primary risk factor for malignancy. In general, the bigger the polyp, the greater the risk for malignancy. There are 3 basic options for removal: standard polypectomy; advanced resection techniques, known as endoscopic mucosal resection (EMR) and endoscopic submucosal dissection (ESD); and surgical removal. In the past 10 years, the use of surgical removal has significantly decreased. Noninvasive, nonmalignant polyps can be removed endoscopically. EMR and ESD are very effective and achieve similar clinical outcomes. Both procedures begin with a submucosal injection. The submucosal lift is one of the most significant advances that have been made in polypectomy. Traditionally, the approach to achieving a submucosal lift has relied on the use of a saline solution. Saline is inexpensive and widely available, but it dissipates quickly. Various viscous agents have been added to saline to maintain mucosal lifting throughout the procedure. Although most are effective, they are used off-label. The only solution approved by the US Food and Drug Administration for the submucosal lift procedure is Eleview. In a clinical trial, Eleview decreased the mean total injected volume and the mean total injected volume per lesion as compared with saline. Other advances in polypectomy techniques include the use of cold snare polypectomy and high-definition colonoscopes. The quality of the colonoscopy can also be improved if a physician knows and monitors his or her adenoma detection rate.
| S-EPMC5721691 | biostudies-other
Project description:Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) with and without designed internal controls.
2023-05-23 | GSE230475 | GEO
Project description:Accurate reconstruction of ancestral states is a critical evolutionary analysis when studying ancient proteins and comparing biochemical properties between parental or extinct species and their extant relatives. It relies on multiple sequence alignment (MSA) which may introduce biases, and it remains unknown how MSA methodological approaches impact ancestral sequence reconstruction (ASR). Here, we investigate how MSA methodology modulates ASR using a simulation study of various evolutionary scenarios. We evaluate the accuracy of ancestral protein sequence reconstruction for simulated data and compare reconstruction outcomes using different alignment methods. Our results reveal biases introduced not only by aligner algorithms and assumptions, but also tree topology and the rate of insertions and deletions. Under many conditions we find no substantial differences between the MSAs. However, increasing the difficulty for the aligners can significantly impact ASR. The MAFFT consistency aligners and PRANK variants exhibit the best performance, whereas FSA displays limited performance. We also discover a bias towards reconstructed sequences longer than the true ancestors, deriving from a preference for inferring insertions, in almost all MSA methodological approaches. In addition, we find measures of MSA quality generally correlate highly with reconstruction accuracy. Thus, we show MSA methodological differences can affect the quality of reconstructions and propose MSA methods should be selected with care to accurately determine ancestral states with confidence.
| S-EPMC5995191 | biostudies-literature
Project description:Genomic selection (GS) has great potential to increase genetic gain in aquaculture breeding; however, its implementation is hindered owing to high genotyping cost and the large number of individuals to genotype. This study investigated the efficiency of genomic prediction in four aquaculture species. In total, 749 to 1481 individuals with records for disease resistance and growth traits were genotyped using SNP arrays ranging from 12K to 40K. We compared the prediction accuracies and bias of breeding values obtained from BLUP, genomic BLUP (GBLUP), Bayesian mixture (BayesR), weighted GBLUP (WGBLUP), and genomic feature BLUP (GFBLUP). For GFBLUP, the genomic feature matrix was constructed based on prior information from genome-wide association studies. Fivefold cross-validation was performed with 20 replicates. Moreover, to reduce the cost of GS, we reduced the SNP density based on linkage disequilibrium as well as the reference population size. The results showed that the methods with marker information produced more accurate predictions than the pedigree-based BLUP method. For the genomic model, BayesR performed prediction with a similar or higher accuracy compared to GBLUP. For the four traits, WGBLUP yielded an average of 1.5% higher accuracy than GBLUP. However, the accuracy of genomic prediction decreased by an average of 6.2% for GFBLUP compared to GBLUP. When the density of SNP panels was reduced to 3K, which was sufficient to obtain accuracies similar to those using the whole dataset in the four species, the cost of GS was estimated to be 50% lower than that of genotyping all animals with high-density panels. In addition, when the reference population size was reduced by 10%, evenly from full-sib family, the accuracy of genomic prediction was almost unchanged, and the cost reduction was 8% in the four populations. Our results have important implications for translating the benefits of GS to most aquaculture species.
| S-EPMC9046917 | biostudies-literature
Project description:Children who use advanced arithmetic strategies, such as count-on and decomposition, are more accurate when solving arithmetic problems and are more likely to later have higher levels of math achievement. The present study tested the hypothesis that instruction using linear-spatial representations would activate children's knowledge necessary for use of mental addition strategies and, thus, lead to greater accuracy on addition problems, than instruction using irregular representations of magnitude. As predicted, low-income kindergartners (n = 29) randomly assigned to practice sums up to 10 using materials that instantiated the linear-spatial features of a mental number line (i.e., discrete squares arranged in rows) demonstrated substantially more improvement in solving unpracticed addition problems than children who practiced with irregular materials (i.e., pictures of stars arranged in random arrays). This was particularly true for children with better initial numerical knowledge, which provided support for the idea that existing knowledge was activated. The use of count-on more than doubled from pretest to posttest among children in the linear-spatial condition and this mediated the difference in improvement between conditions. The importance of aligning instructional materials to relevant mental representations-consistent with the Cognitive Alignment Framework for instructional design-is discussed.
| S-EPMC6312299 | biostudies-literature
Project description:In our study, we proposed first to reduce the profiling variability by selecting the miRNA isolation kit offering the higher input RNA concentration for microarray profiling and second to control the profiling step variability by adapting the widely used exogenous normalization of the validation step to the profiling one. The new strategy proposed could improve the overlap between independent studies using microarray profiling, but also potentially with other high-throughput methods, to finally identify pertinent miRNA signatures in biofluids. Because this project is only a methodological study, the cohort of serum and plasma samples used in this study were all obtained from patients with FIGO stages III/IV serous ovarian cancer. This study was approved by the ethics committee Nord-Ouest III [CPP N° 2011-02] and national authorities (AFSSAPS N°B110260-20). Plasma samples were obtained from the Comprehensive Cancer Center F. Baclesse biological collections that have been declared (# DC-2010-1243) to the French Ministry of Research and Superior Education. Prior to scientific use of samples and data, patients were appropriately informed and asked to consent in writing, in compliance with French and European regulations.
2016-06-30 | GSE69341 | GEO
Project description:While most of the recent improvements in multiple sequence alignment accuracy are due to better use of vertical information, which include the incorporation of consistency-based pairwise alignments and the use of profile alignments, we observe that it is possible to further improve accuracy by taking into account alignment of neighboring residues when aligning two residues, thus making better use of horizontal information. By modifying existing multiple alignment algorithms to make use of horizontal information, we show that this strategy is able to consistently improve over existing algorithms on a few sets of benchmark alignments that are commonly used to measure alignment accuracy, and the average improvements in accuracy can be as much as 1-3% on protein sequence alignment and 5-10% on DNA/RNA sequence alignment. Unlike previous algorithms, consistent average improvements can be obtained across all identity levels.
| S-EPMC2632924 | biostudies-literature
Project description:Ancestral sequence reconstruction (ASR) uses an alignment of extant protein sequences, a phylogeny describing the history of the protein family and a model of the molecular-evolutionary process to infer the sequences of ancient proteins, allowing researchers to directly investigate the impact of sequence evolution on protein structure and function. Like all statistical inferences, ASR can be sensitive to violations of its underlying assumptions. Previous studies have shown that, whereas phylogenetic uncertainty has only a very weak impact on ASR accuracy, uncertainty in the protein sequence alignment can more strongly affect inferred ancestral sequences. Here, we show that errors in sequence alignment can produce errors in ASR across a range of realistic and simplified evolutionary scenarios. Importantly, sequence reconstruction errors can lead to errors in estimates of structural and functional properties of ancestral proteins, potentially undermining the reliability of analyses relying on ASR. We introduce an alignment-integrated ASR approach that combines information from many different sequence alignments. We show that integrating alignment uncertainty improves ASR accuracy and the accuracy of downstream structural and functional inferences, often performing as well as highly accurate structure-guided alignment. Given the growing evidence that sequence alignment errors can impact the reliability of ASR studies, we recommend that future studies incorporate approaches to mitigate the impact of alignment uncertainty. Probabilistic modeling of insertion and deletion events has the potential to radically improve ASR accuracy when the model reflects the true underlying evolutionary history, but further studies are required to thoroughly evaluate the reliability of these approaches under realistic conditions.
| S-EPMC7523730 | biostudies-literature
Project description:BACKGROUND:Long reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days to process datasets enough to sequence a human genome on a single node. Hence, it is of primary importance to have an aligner which can operate on distributed clusters of computers with high performance in accuracy and speed. RESULTS:In this paper, we presented IMOS, an aligner for mapping noisy long reads to the reference genome. It can be used on a single node as well as on distributed nodes. In its single-node mode, IMOS is an Improved version of Meta-aligner (IM) enhancing both its accuracy and speed. IM is up to 6x faster than the original Meta-aligner. It is also implemented to run IM and Minimap2 on Apache Spark for deploying on a cluster of nodes. Moreover, multi-node IMOS is faster than SparkBWA while executing both IM (1.5x) and Minimap2 (25x). CONCLUSION:In this paper, we purposed an architecture for mapping long reads to a reference. Due to its implementation, IMOS speed can increase almost linearly with respect to the number of nodes in a cluster. Also, it is a multi-platform application able to operate on Linux, Windows, and macOS.
| S-EPMC6345043 | biostudies-literature