icHET: interactive visualization of cytoplasmic heteroplasmy

2019 ◽  
Vol 35 (21) ◽  
pp. 4411-4412 ◽  
Author(s):  
Vinhthuy Phan ◽  
Diem-Trang Pham ◽  
Caroline Melton ◽  
Adam J Ramsey ◽  
Bernie J Daigle ◽  
...  
Keyword(s):  
Reference Genome ◽  
Interactive Visualization ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Short Reads ◽  
Genome Wide ◽  
Computational Workflow ◽  
Multiple Samples

Abstract Summary Although heteroplasmy has been studied extensively in animal systems, there is a lack of tools for analyzing, exploring and visualizing heteroplasmy at the genome-wide level in other taxonomic systems. We introduce icHET, which is a computational workflow that produces an interactive visualization that facilitates the exploration, analysis and discovery of heteroplasmy across multiple genomic samples. icHET works on short reads from multiple samples from any organism with an organellar reference genome (mitochondrial or plastid) and a nuclear reference genome. Availability and implementation The software is available at https://github.com/vtphan/HeteroplasmyWorkflow. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Visualization of circular RNAs and their internal splicing events from transcriptomic data

2020 ◽  
Vol 36 (9) ◽  
pp. 2934-2935 ◽  
Author(s):  
Yi Zheng ◽  
Fangqing Zhao
Keyword(s):  
Supplementary Information ◽  
Circular Rnas ◽  
Visualization Tool ◽  
Command Line ◽  
Supplementary Data ◽  
Transcriptomic Data ◽  
Command Line Tool ◽  
Transcriptome Comparison ◽  
Multiple Samples ◽  
Splicing Patterns

Abstract Summary Circular RNAs (circRNAs) are proved to have unique compositions and splicing events distinct from canonical mRNAs. However, there is no visualization tool designed for the exploration of complex splicing patterns in circRNA transcriptomes. Here, we present CIRI-vis, a Java command-line tool for quantifying and visualizing circRNAs by integrating the alignments and junctions of circular transcripts. CIRI-vis can be applied to visualize the internal structure and isoform abundance of circRNAs and perform circRNA transcriptome comparison across multiple samples. Availability and implementation https://sourceforge.net/projects/ciri/files/CIRI-vis. Supplementary information Supplementary data are available at Bioinformatics online.

Minirmd: accurate and fast duplicate removal tool for short reads via multiple minimizers

2020 ◽  
Author(s):  
Yuansheng Liu ◽  
Xiaocai Zhang ◽  
Quan Zou ◽  
Xiangxiang Zeng
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Complementary Strand ◽  
Short Reads ◽  
Sequencing Technologies ◽  
Computational Resources

Abstract Summary Removing duplicate and near-duplicate reads, generated by high-throughput sequencing technologies, is able to reduce computational resources in downstream applications. Here we develop minirmd, a de novo tool to remove duplicate reads via multiple rounds of clustering using different length of minimizer. Experiments demonstrate that minirmd removes more near-duplicate reads than existing clustering approaches and is faster than existing multi-core tools. To the best of our knowledge, minirmd is the first tool to remove near-duplicates on reverse-complementary strand. Availability and implementation https://github.com/yuansliu/minirmd. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps

2019 ◽  
Vol 35 (16) ◽  
pp. 2724-2729 ◽  
Author(s):  
L Carron ◽  
J B Morlot ◽  
V Matthys ◽  
A Lesne ◽  
J Mozziconacci
Keyword(s):  
Long Range ◽  
Short Range ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Missing Information ◽  
High Confidence ◽  
Contact Maps ◽  
Genome Wide ◽  
Algorithmic Procedure

Abstract Motivation Genome-wide chromosomal contact maps are widely used to uncover the 3D organization of genomes. They rely on collecting millions of contacting pairs of genomic loci. Contacts at short range are usually well measured in experiments, while there is a lot of missing information about long-range contacts. Results We propose to use the sparse information contained in raw contact maps to infer high-confidence contact counts between all pairs of loci. Our algorithmic procedure, Boost-HiC, enables the detection of Hi-C patterns such as chromosomal compartments at a resolution that would be otherwise only attainable by sequencing a hundred times deeper the experimental Hi-C library. Boost-HiC can also be used to compare contact maps at an improved resolution. Availability and implementation Boost-HiC is available at https://github.com/LeopoldC/Boost-HiC. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals pyseer: a comprehensive tool for microbial pangenome-wide association studies

2018 ◽  
Author(s):  
John A Lees ◽  
Marco Galardini ◽  
Stephen D Bentley ◽  
Jeffrey N Weiser ◽  
Jukka Corander
Keyword(s):  
Input Data ◽  
Association Studies ◽  
Genome Wide Association ◽  
Supplementary Information ◽  
Genome Wide Association Studies ◽  
Supplementary Data ◽  
New Methods ◽  
Link Type ◽  
Genome Wide

AbstractSummaryGenome-wide association studies (GWAS) in microbes face different challenges to eukaryotes and have been addressed by a number of different methods. pyseer brings these techniques together in one package tailored to microbial GWAS, allows greater flexibility of the input data used, and adds new methods to interpret the association results.Availability and Implementationpyseer is written in python and is freely available at https://github.com/mgalardini/pyseer, or can be installed through pip. Documentation and a tutorial are available at http://[email protected] and [email protected] informationSupplementary data are available online.

scholarly journals Rapid epistatic mixed-model association studies by controlling multiple polygenic effects

2020 ◽  
Vol 36 (19) ◽  
pp. 4833-4837
Author(s):  
Dan Wang ◽  
Hui Tang ◽  
Jian-Feng Liu ◽  
Shizhong Xu ◽  
Qin Zhang ◽  
...  
Keyword(s):  
Mixed Model ◽  
Association Studies ◽  
Approximate Algorithm ◽  
Supplementary Information ◽  
Simulation Studies ◽  
Supplementary Data ◽  
Source Codes ◽  
Pairwise Interactions ◽  
Genome Wide ◽  
Model Algorithm

Abstract Summary We have developed a rapid mixed model algorithm for exhaustive genome-wide epistatic association analysis by controlling multiple polygenic effects. Our model can simultaneously handle additive by additive epistasis, dominance by dominance epistasis and additive by dominance epistasis, and account for intrasubject fluctuations due to individuals with repeated records. Furthermore, we suggest a simple but efficient approximate algorithm, which allows the examination of all pairwise interactions in a remarkably fast manner of linear with population size. Simulation studies are performed to investigate the properties of REMMAX. Application to publicly available yeast and human data has showed that our mixed model-based method has similar performance with simple linear model on computational efficiency. It took less than 40 h for the pairwise analysis of 5000 individuals genotyped with roughly 350 000 SNPs with five threads on Intel Xeon E5 2.6 GHz CPU. Availability and implementation Source codes are freely available at https://github.com/chaoning/GMAT. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CNValidator: validating somatic copy-number inference

2018 ◽  
Vol 35 (15) ◽  
pp. 2660-2662
Author(s):  
Lucian P Smith ◽  
Jon A Yamato ◽  
Mary K Kuhner
Keyword(s):  
Data Quality ◽  
Copy Number ◽  
Supplementary Information ◽  
Tuning Parameter ◽  
Supplementary Data ◽  
Calling Algorithm ◽  
Quality Issues ◽  
Multiple Samples ◽  
Parameter Values

Abstract Motivation CNValidator assesses the quality of somatic copy-number calls based on coherency of haplotypes across multiple samples from the same individual. It is applicable to any copy-number calling algorithm, which makes calls independently for each sample. This test is useful in assessing the accuracy of copy-number calls, as well as choosing among alternative copy-number algorithms or tuning parameter values. Results On a dataset of somatic samples from individuals with Barrett’s Esophagus, CNValidator provided feedback on the correctness of sample ploidy calls and also detected data quality issues. Availability and implementation CNValidator is available on GitHub at https://github.com/kuhnerlab/CNValidator. Supplementary information Supplementary data are available at Bioinformatics online.

EpiGEN: an epistasis simulation pipeline

2020 ◽  
Vol 36 (19) ◽  
pp. 4957-4959
Author(s):  
David B Blumenthal ◽  
Lorenzo Viola ◽  
Markus List ◽  
Jan Baumbach ◽  
Paolo Tieri ◽  
...  
Keyword(s):  
Arbitrary Order ◽  
Association Studies ◽  
Simulated Data ◽  
Genome Wide Association ◽  
Supplementary Information ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Supplementary Data ◽  
Single Nucleotide ◽  
Genome Wide

Abstract Summary Simulated data are crucial for evaluating epistasis detection tools in genome-wide association studies. Existing simulators are limited, as they do not account for linkage disequilibrium (LD), support limited interaction models of single nucleotide polymorphisms (SNPs) and only dichotomous phenotypes or depend on proprietary software. In contrast, EpiGEN supports SNP interactions of arbitrary order, produces realistic LD patterns and generates both categorical and quantitative phenotypes. Availability and implementation EpiGEN is implemented in Python 3 and is freely available at https://github.com/baumbachlab/epigen. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals HaploTypo: a variant-calling pipeline for phased genomes

2019 ◽  
Vol 36 (8) ◽  
pp. 2569-2571 ◽  
Author(s):  
Cinta Pegueroles ◽  
Verónica Mixão ◽  
Laia Carreté ◽  
Manu Molina ◽  
Toni Gabaldón
Keyword(s):  
Genetic Variation ◽  
Genetic Variant ◽  
Reference Genome ◽  
Variant Calling ◽  
Supplementary Information ◽  
Haplotype Structure ◽  
Supplementary Data ◽  
Heterozygous Variant ◽  
Reference Genomes

Abstract Summary An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome. Availability and implementation HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Nubeam-dedup: a fast and RAM-efficient tool to de-duplicate sequencing reads without mapping

2020 ◽  
Vol 36 (10) ◽  
pp. 3254-3256 ◽  
Author(s):  
Hang Dai ◽  
Yongtao Guan
Keyword(s):  
Hash Function ◽  
Reference Genome ◽  
State Of The Art ◽  
Source Code ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Efficient Tool ◽  
Cpu Time ◽  
Products Of Matrices

Abstract Summary We present Nubeam-dedup, a fast and RAM-efficient tool to de-duplicate sequencing reads without reference genome. Nubeam-dedup represents nucleotides by matrices, transforms reads into products of matrices, and based on which assigns a unique number to a read. Thus, duplicate reads can be efficiently removed by using a collisionless hash function. Compared with other state-of-the-art reference-free tools, Nubeam-dedup uses 50–70% of CPU time and 10–15% of RAM. Availability and implementation Source code in C++ and manual are available at https://github.com/daihang16/nubeamdedup and https://haplotype.org. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Assembly Graph Browser: interactive visualization of assembly graphs

2019 ◽  
Vol 35 (18) ◽  
pp. 3476-3478 ◽  
Author(s):  
Alla Mikheenko ◽  
Mikhail Kolmogorov
Keyword(s):  
Genome Assembly ◽  
Open Problem ◽  
Interactive Visualization ◽  
Supplementary Information ◽  
Supplementary Data ◽  
New Approach ◽  
Repeat Analysis

Abstract Summary Currently, most genome assembly projects focus on contigs and scaffolds rather than assembly graphs that provide a more comprehensive representation of an assembly. Since interactive visualization of large assembly graphs remains an open problem, we developed an Assembly Graph Browser (AGB) tool that visualizes large assembly graphs, extending the functionality of previously developed visualization approaches. Assembly Graph Browser includes a number of novel functions including repeat analysis, construction of the contracted assembly graphs (i.e. the graphs obtained by collapsing a selected set of edges) and a new approach to visualizing large assembly graphs. Availability and implementation http://www.github.com/almiheenko/AGB. Supplementary information Supplementary data are available at Bioinformatics online.

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