Training alignment parameters for arbitrary sequencers with LAST-TRAIN.
Ontology highlight
ABSTRACT:
SUBMITTER: Hamada M
PROVIDER: S-EPMC5351549 | biostudies-literature | 2017 Mar
REPOSITORIES: biostudies-literature
Publications
Training alignment parameters for arbitrary sequencers with LAST-TRAIN.
Hamada Michiaki M Ono Yukiteru Y Asai Kiyoshi K Frith Martin C MC
Bioinformatics (Oxford, England) 20170301 6
<h4>Summary</h4>LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads.<h4>Availability and implementation</h4>the source code is freely available at http://last.cbrc.jp/.<h4>Contact</h4>mhamada@waseda.jp or mcfrith@edu.k.u-tokyo.ac.jp.< ...[more]
Similar Datasets
Project description:BACKGROUND: Genome sequence alignments form the basis of much research. Genome alignment depends on various mundane but critical choices, such as how to mask repeats and which score parameters to use. Surprisingly, there has been no large-scale assessment of these choices using real genomic data. Moreover, rigorous procedures to control the rate of spurious alignment have not been employed. RESULTS: We have assessed 495 combinations of score parameters for alignment of animal, plant, and fungal genomes. As our gold-standard of accuracy, we used genome alignments implied by multiple alignments of proteins and of structural RNAs. We found the HOXD scoring schemes underlying alignments in the UCSC genome database to be far from optimal, and suggest better parameters. Higher values of the X-drop parameter are not always better. E-values accurately indicate the rate of spurious alignment, but only if tandem repeats are masked in a non-standard way. Finally, we show that gamma-centroid (probabilistic) alignment can find highly reliable subsets of aligned bases. CONCLUSIONS: These results enable more accurate genome alignment, with reliability measures for local alignments and for individual aligned bases. This study was made possible by our new software, LAST, which can align vertebrate genomes in a few hours http://last.cbrc.jp/.
| S-EPMC2829014 | biostudies-literature
Project description:UnlabelledTwo methods to add unaligned sequences into an existing multiple sequence alignment have been implemented as the '--add' and '--addfragments' options in the MAFFT package. The former option is a basic one and applicable only to full-length sequences, whereas the latter option is applicable even when the unaligned sequences are short and fragmentary. These methods internally infer the phylogenetic relationship among the sequences in the existing alignment and the phylogenetic positions of unaligned sequences. Benchmarks based on two independent simulations consistently suggest that the "--addfragments" option outperforms recent methods, PaPaRa and PAGAN, in accuracy for difficult problems and that these three methods appropriately handle easy problems.Availabilityhttp://mafft.cbrc.jp/alignment/software/Contactkatoh@ifrec.osaka-u.ac.jpSupplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC3516148 | biostudies-literature
Project description:Cylindrically polarized (CP) modes are laser beam modes which have rotational symmetry of the polarization distribution around the beam axis. Considerable attention has been paid to CP modes for their various applications. In this paper, by using the extended Stokes parameters and the degree of polarization defined for the spatial distribution (DOP-SD), we fully-quantitatively characterize the spectrally-resolved polarization states of arbitrary CP (axisymmetrically polarized and higher-order cylindrically polarized) broadband pulses generated by coherent beam combining. All the generated pulse states were fully-quantitatively analyzed for the first time and proved to have high symmetry (DOP-SD???0.95) and low spectral dependence of polarization states. Moreover, we show the DOP-SD, which cannot be defined by the conventional higher-order and hybrid Stokes parameters, enables us to make a quantitative evaluation of small degradation of rotational symmetry of polarization distribution. This quantitative characterization with high precision is significant for applications of precise material processing, quantum information processing, magneto-optical storage and nonlinear spectroscopic polarimetry.
| S-EPMC4674746 | biostudies-literature
Project description:MotivationMost sequence alignment techniques make use of exact k-mer hits, called seeds, as anchors to optimize alignment speed. A large number of bioinformatics tools employing seed-based alignment techniques, such as Minimap2, use a single value of k per sequencing technology, without a strong guarantee that this is the best possible value. Given the ubiquity of sequence alignment, identifying values of k that lead to more sensitive alignments is thus an important task. To aid this, we present Seedability, a seed-based alignment framework designed for estimating an optimal seed k-mer length (as well as a minimal number of shared seeds) based on a given alignment identity threshold. In particular, we were motivated to make Minimap2 more sensitive in the pairwise alignment of short sequences.ResultsThe experimental results herein show improved alignments of short and divergent sequences when using the parameter values determined by Seedability in comparison to the default values of Minimap2. We also show several cases of pairs of real divergent sequences, where the default parameter values of Minimap2 yield no output alignments, but the values output by Seedability produce plausible alignments.Availability and implementationhttps://github.com/lorrainea/Seedability (distributed under GPL v3.0).
| S-EPMC10444664 | biostudies-literature
Project description:Teacher training programmes are necessary assets in faculty development. Few data exist on their long-term effects on participants' teaching skills. Our aim was to study participants' didactic competencies up to four years after attending a newly established faculty development workshop at Hamburg Medical School. Of the 322 participants who attended our teacher training between 2006 and 2009, 313 received a self-assessment and evaluation questionnaire in 2010. This follow-up self-assessment (t2) was compared with their self-assessment of the same didactic competencies before (t0) and directly after (t1) the training. Correlations between participants' personal reasons to attend the workshop and their assessment of didactic competencies were investigated. Self-assessment was significantly higher at the time of follow-up (t2) for all cohorts compared to the assessment before the workshop (t0). Personal reasons for participation differed greatly between voluntary and mandatory. However, self-assessment of the didactic competencies (t2) was not different between these groups. Participants involved in objective structured clinical examinations (OSCE) rated their competency in this field higher than participants without OSCE involvement. In conclusion, teacher training can be effective in the long run even when participation is mandatory. Competencies seem to be retained best when the content of the training fits participants' teaching activities.
| S-EPMC3778536 | biostudies-other
Project description:BackgroundThe first wave of the SARS-CoV-2 global pandemic in early 2020 required a rapid roll-out of infection prevention and control (IPC) training for healthcare workers (HCW), including use of appropriate personal protective equipment (PPE). Education about respiratory droplet and aerosol transmission was of paramount importance to ensure safe working practices and improve confidence.MethodsA joint working group of Infectious Diseases and IPC staff developed a 'train the trainers' programme, to be rapidly deployed over a three-week period. This model utilised a snowballing approach, training selected staff with the intention that they would train their teams, facilitating swift cascading of information. Targeted invitations prompted staff from diverse departments of the hospital to attend. Pre- and post-session questionnaires evaluated staff confidence with regard to appropriate PPE use.ResultsThe programme trained 130 HCW over a three week period, was well received and led to increased confidence with PPE use amongst staff. Real-time evaluation ensured content could be adapted to the specific needs of HCW involved. We highlight perceived gaps in training despite existing and enhanced training structures.ConclusionProvision of face-to-face training in transmission-based precautions, including PPE use, is required to maintain confidence in safe and appropriate IPC amongst hospital staff. We highlight the importance of including non-clinical staff in PPE educational programmes, recognising that these roles are vital for patient care and are frequently patient-facing. We recommend adopting the train the trainers model to facilitate rapid dissemination of education, with interactive multidisciplinary training in future outbreaks to improve HCW confidence and effective IPC.
| S-EPMC10148243 | biostudies-literature
Project description:One of the main goals of the ELIXIR-EXCELERATE project from the European Union's Horizon 2020 programme is to support a pan-European training programme to increase bioinformatics capacity and competency across ELIXIR Nodes. To this end, a Train-the-Trainer (TtT) programme has been developed by the TtT subtask of EXCELERATE's Training Platform, to try to expose bioinformatics instructors to aspects of pedagogy and evidence-based learning principles, to help them better design, develop and deliver high-quality training in future. As a first step towards such a programme, an ELIXIR-EXCELERATE TtT (EE-TtT) pilot was developed, drawing on existing 'instructor training' models, using input both from experienced instructors and from experts in bioinformatics, the cognitive sciences and educational psychology. This manuscript describes the process of defining the pilot programme, illustrates its goals, structure and contents, and discusses its outcomes. From Jan 2016 to Jan 2017, we carried out seven pilot EE-TtT courses (training more than sixty new instructors), collaboratively drafted the training materials, and started establishing a network of trainers and instructors within the ELIXIR community. The EE-TtT pilot represents an essential step towards the development of a sustainable and scalable ELIXIR TtT programme. Indeed, the lessons learned from the pilot, the experience gained, the materials developed, and the analysis of the feedback collected throughout the seven pilot courses have both positioned us to consolidate the programme in the coming years, and contributed to the development of an enthusiastic and expanding ELIXIR community of instructors and trainers.
| S-EPMC5596339 | biostudies-literature
Project description:A comprehensive data set of aligned ligands with highly similar binding pockets from the Protein Data Bank has been built. Based on this data set, a scoring function for recognizing good alignment poses for small molecules has been developed. This function is based on atoms and hydrogen-bond projected features. The concept is simply that atoms and features of a similar type (hydrogen-bond acceptors/donors and hydrophobic) tend to occupy the same space in a binding pocket and atoms of incompatible types often tend to avoid the same space. Comparison with some recently published results of small molecule alignments shows that the current scoring function can lead to performance better than those of several existing methods.
| S-EPMC2946173 | biostudies-literature
Project description:IntroductionThis paper reports on the effects of a 9-week vitality training that employed behaviour-change techniques and was evaluated using a randomised controlled trial (RCT) in three large companies based in the Netherlands.MethodsA total of 84 adult employees from three participating organisations in the Netherlands were enrolled in the study. A parallel group RCT design was employed and participants were assigned using individual random assignment to either an intervention (n = 38) or a waitlist control group (n = 46). The intervention consisted of a 9-week vitality training employing the behaviour-change techniques of self-persuasion, implementation intentions, and self-efficacy, which was delivered in-house over five fortnightly 2-hour sessions. Primary outcomes (i.e., reported energy and stress) and secondary outcomes (i.e., reported daily life satisfaction and work capacity) were assessed prior to, immediately after, and 3 months following the intervention.ResultsA mixed MANOVA revealed a significant interaction effect between treatment group and time period for the combination of reported energy, stress, daily life satisfaction, and work capacity. Subsequent univariate ANOVAs revealed significant interactions between treatment group and time period for reported energy, stress, and daily life satisfaction; however, not for reported work capacity. Improvements in outcomes were observed for both groups following their completion of the vitality training; however, not all improvements reached statistical significance. Reported self-efficacy regarding managing work-life balance was found to mediate the relationship between the effects of the intervention and reported energy; however, such an effect was not found for stress.DiscussionAn intervention drawing upon evidence-based behaviour-change techniques shows promise for improving indicators associated with burnout; although, it is recommended that in future research a larger-scale evaluation be conducted over a longer time period with an active control group to establish effectiveness.Clinical trial registration: https://www.anzctr.org.au/, ACTRN12622001268730.
| S-EPMC10826839 | biostudies-literature