scholarly journals MitoZ: A toolkit for mitochondrial genome assembly, annotation and visualization

2018 ◽  
Author(s):  
Guanliang Meng ◽  
Yiyuan Li ◽  
Chentao Yang ◽  
Shanlin Liu
Keyword(s):  
Mitochondrial Genome ◽  
Open Source Software ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Ecological Studies ◽  
Free Open Source Software ◽  
Sequencing Technologies ◽  
Evolutionary Studies ◽  
Free Open Source

AbstractMitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules ofde novoassembly, findMitoScaf, annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available athttps://github.com/linzhi2013/MitoZ.

scholarly journals MiniScrub: de novo long read scrubbing using approximate alignment and deep learning

2018 ◽  
Author(s):  
Nathan LaPierre ◽  
Rob Egan ◽  
Wei Wang ◽  
Zhong Wang
Keyword(s):  
Open Source Software ◽  
Genome Assembly ◽  
Large Scale ◽  
Structural Variation ◽  
De Novo ◽  
Error Rates ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Reference Genomes

AbstractLong read sequencing technologies such as Oxford Nanopore can greatly de-crease the complexity of de novo genome assembly and large structural variation iden-tification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. Many methods for resolving these errors require access to reference genomes, high-fidelity short reads, or reference genomes, which are often not available. De novo error correction modules are available, often as part of assembly tools, but large-scale errors still remain in resulting assemblies, motivating further innovation in this area. We developed a novel Convolutional Neu-ral Network (CNN) based method, called MiniScrub, for de novo identification and subsequent “scrubbing” (removal) of low-quality Nanopore read segments. MiniScrub first generates read-to-read alignments by MiniMap, then encodes the alignments into images, and finally builds CNN models to predict low-quality segments that could be scrubbed based on a customized quality cutoff. Applying MiniScrub to real world con-trol datasets under several different parameters, we show that it robustly improves read quality. Compared to raw reads, de novo genome assembly with scrubbed reads pro-duces many fewer mis-assemblies and large indel errors. 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

Abstract 17081: End Stage Mitochondrial Cardiomyopathy And Heart Transplantation Due To Pathogenic Biallelic C1QBP Variants

Circulation ◽  
2021 ◽  
Vol 144 (Suppl_2) ◽  
Author(s):  
Nicholas S Wilcox ◽  
Stuart Prenner ◽  
Marisa Cevasco ◽  
Courtney Condit ◽  
Amy Goldstein ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Heart Transplantation ◽  
Genome Sequencing ◽  
Large Scale ◽  
De Novo ◽  
Late Onset ◽  
Genetic Disorder ◽  
Disease Onset ◽  
Serum Lactate ◽  
Metabolic Decompensation

Case Presentation: A 29-year-old male with LVH diagnosed in childhood was admitted with acute HF. TTE showed LVEF 5-10% and LV thrombi for which he was anticoagulated. He received inappropriate ICD shocks due to T wave oversensing, leading to cardiogenic shock requiring VA-ECMO support. Serum lactate peaked at 17 mmol/L due to cardiac and metabolic decompensation. He underwent heart transplantation (HT) on hospital day (HD) 8 and tolerated standard immunosuppression. First endomyocardial biopsy showed acute cellular rejection requiring pulse steroids. He was discharged on HD 33. Trio whole exome and mitochondrial genome sequencing revealed biallelic variants in complement component 1Q subcomponent-binding protein ( C1QBP ), due to a maternally inherited likely pathogenic variant c.612C>G (p.F204L in exon 5) and an apparently de novo deletion of 17p13.2, spanning exons 4-6 of C1QBP and exon 6 of the RPAIN gene. Mitochondrial genome sequencing of the explanted heart revealed multiple large-scale mitochondrial DNA deletions at 33% heteroplasmy. Discussion: C1QBP variants are associated with mitochondrial and multi-organ dysfunction. Only 12 patients exhibiting biallelic C1QBP variants are reported. Four died in the peripartum period due to fetal hydrops or HF; 5 exhibited early-onset cardiomyopathy (CM); 3 others had late-onset ophthalmoplegia without CM. The p.F204L variant has been reported in 1 patient with compound C1QBP p.F204L/p.C186S heterozygosity who died from hydrops fetalis and a second with p.F204L homozygosity with late-onset ophthalmoplegia and skeletal myopathy without CM. Differences in the size, heteroplasmy, and tissue distribution of mitochondrial genome secondary deletions may explain variability in disease onset and progression. We present the first patient with biallelic pathogenic C1QBP gene variants with mitochondrial CM to undergo HT and highlight the diagnosis and management of an exceptionally uncommon genetic disorder.

scholarly journals SENTIMENT ANALYSIS OF FREE/OPEN SOURCE DEVELOPERS: PRELIMINARY FINDINGS FROM A CASE STUDY

2014 ◽  
Vol 13 (2) ◽  
Author(s):  
Athanasios-Ilias Rousinopoulos ◽  
Gregorio Robles ◽  
Jesús M. González-Barahona
Keyword(s):  
Sentiment Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Free Open Source Software ◽  
Free Open Source

O desenvolvimento de software é uma atividade intensive em esforço humano. Assim, a forma como os desenvolvedores encaram suas tarefas é de suam importância. Em um ambiente como o usual em projetos de FOSS (free/open source software) em que profissionais (desenvolvedores pagos) compartilham os esforços de desenvolvimento com voluntários, a moral da comunidade de desenvolvedores e usuários é fundamental. Neste artigo, apresentamos uma análise preliminary utilizando técnicas de análise de sentimentos realizada em um projeto de FOSS. Para isso, executamos a mineração da lista de endereços eletrônicos de um projeto e aplicamos as técnicas propostas aos participantes mais relevantes. Embora a aplicação seja limitada, no momento atual, experamos que essa experiência possa ser benéfica no future para determiner situações que possam afetar os desenvolvedores ou o projeto, tais como baixa produtividade, abandono do projeto ou bifurcação do projeto, entre outras.

scholarly journals Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2006
Author(s):  
Anna Y Budkina ◽  
Elena V Korneenko ◽  
Ivan A Kotov ◽  
Daniil A Kiselev ◽  
Ilya V Artyushin ◽  
...  
Keyword(s):  
Large Scale ◽  
High Throughput Sequencing ◽  
Metagenomic Data ◽  
Sequencing Data ◽  
Viral Pathogens ◽  
Genomic Databases ◽  
Bioinformatic Pipeline ◽  
Viral Genomes ◽  
Sequencing Technologies ◽  
Viral Screening

According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.

scholarly journals CACTI: Free, Open-Source Software for the Sequential Coding of Behavioral Interactions

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e39740 ◽  
Author(s):  
Lisa H. Glynn ◽  
Kevin A. Hallgren ◽  
Jon M. Houck ◽  
Theresa B. Moyers
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Behavioral Interactions ◽  
Free Open Source Software ◽  
Free Open Source
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