scholarly journals KmerFinderJS: A client-server method for fast species typing of bacteria over slow Internet connections

2017 ◽  
Author(s):  
Jose Luis Bellod Cineros ◽  
Ole Lund
Keyword(s):  
Bacterial Species ◽  
Source Code ◽  
Supplementary Information ◽  
The Internet ◽  
Supplementary Data ◽  
Client Server ◽  
Link Type ◽  
Genome Data ◽  
Speed Up ◽  
Internet Connections

AbstractMotivationKmerFinder is a program based on K-mer statistics for identifying bacterial species in whole genome data, that as a web server that have been used more than 10.000 times. Kmer-FinderJS is a development of the KmerFinder that benefits from the downsampling of data using a prefix filtering used by KmerFinder, to minimize amount of data that needs to be transferred between the client and the server.ResultsKmerFinderJS replaces the python based hash structure for holding the databases with a true Key-value database. These improvements are shown to lead to a many-fold speed up of species identification with the internet transfer speeds that are realistic to expect today. It is also shown that the method can find the true content of an artificial metagenomic cocktail with no false positives.AvailabilityThe method is freely available at https://cge.cbs.dtu.dk/services/KmerFinderJS/ and as a source code at https://bitbucket.org/genomicepidemiology/[email protected] informationSupplementary data are available at biorxiv online.

scholarly journals PhyloFold: Precise and Swift Prediction of RNA Secondary Structures to Incorporate Phylogeny among Homologs

2020 ◽  
Author(s):  
Masaki Tagashira
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Prediction Accuracy ◽  
Structural Alignment ◽  
Source Code ◽  
Secondary Structures ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Link Type ◽  
Structural Alignments

AbstractMotivationThe simultaneous consideration of sequence alignment and RNA secondary structure, or structural alignment, is known to help predict more accurate secondary structures of homologs. However, the consideration is heavy and can be done only roughly to decompose structural alignments.ResultsThe PhyloFold method, which predicts secondary structures of homologs considering likely pairwise structural alignments, was developed in this study. The method shows the best prediction accuracy while demanding comparable running time compared to conventional methods.AvailabilityThe source code of the programs implemented in this study is available on “https://github.com/heartsh/phylofold” and “https://github.com/heartsh/phyloalifold“.Contact“[email protected]”.Supplementary informationSupplementary data are available.

scholarly journals deSPI: efficient classification of metagenomic reads with lightweight de Bruijn graph-based reference indexing

2016 ◽  
Author(s):  
Dengfeng Guan ◽  
Bo Liu ◽  
Yadong Wang
Keyword(s):  
Source Code ◽  
Classification Method ◽  
Supplementary Information ◽  
De Bruijn Graph ◽  
Supplementary Data ◽  
Link Type ◽  
Memory Footprint ◽  
Supplementary Material ◽  
De Bruijn

AbstractSummaryIn metagenomic studies, fast and effective tools are on wide demand to implement taxonomy classification for upto billions of reads. Herein, we propose deSPI, a novel read classification method that classifies reads by recognizing and analyzing the matches between reads and reference with de Bruijn graph-based lightweight reference indexing. deSPI has faster speed with relatively small memory footprint, meanwhile, it can also achieve higher or similar sensitivity and accuracy.Availabilitythe C++ source code of deSPI is available at https://github.com/hitbc/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals hmmIBD: software to infer pairwise identity by descent between haploid genotypes

2017 ◽  
Author(s):  
Stephen F. Schaffner ◽  
Aimee R. Taylor ◽  
Wesley Wong ◽  
Dyann F. Wirth ◽  
Daniel E. Neafsey
Keyword(s):  
Plasmodium Falciparum ◽  
Malaria Parasite ◽  
Source Code ◽  
Simulated Data ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Identity By Descent ◽  
Pairwise Identity ◽  
Link Type

AbstractSummaryWe introduce hmmIBD, software to estimate pairwise identity by decent between haploid genomes, such as those of the malaria parasite, sampled from one or more populations. We verified hmmIBD using simulated data, benchmarked it against a previously published method for detecting IBD within populations, and demonstrated its utility using Plasmodium falciparum data from Cambodia and Ghana.Supplementary informationSupplementary data include Appendices S1, S2 and S3, and are available online.Availability and ImplemetationSource code written in C99/C11-compliant C and requiring no external libraries, is freely available for download at https://github.com/glipsnort/hmmIBD/releases, alongside test [email protected]

KEC: unique sequence search by K-mer exclusion

2021 ◽  
Author(s):  
Pavel Beran ◽  
Dagmar Stehlíková ◽  
Stephen P Cohen ◽  
Vladislav Čurn
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Source Code ◽  
Unique Sequence ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Laptop Computers ◽  
Sequence Search ◽  
Target Sequences ◽  
Cross Reference

Abstract Summary Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications. Availability and implementation KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals BioCommons: a robust java library for RNA structural bioinformatics

2021 ◽  
Author(s):  
Tomasz Zok
Keyword(s):  
Source Code ◽  
Structural Bioinformatics ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Bioinformatic Tools ◽  
Data Formats ◽  
Central Repository ◽  
Diverse Data ◽  
2D And 3D ◽  
Java Library

Abstract Motivation Biomolecular structures come in multiple representations and diverse data formats. Their incompatibility with the requirements of data analysis programs significantly hinders the analytics and the creation of new structure-oriented bioinformatic tools. Therefore, the need for robust libraries of data processing functions is still growing. Results BioCommons is an open-source, Java library for structural bioinformatics. It contains many functions working with the 2D and 3D structures of biomolecules, with a particular emphasis on RNA. Availability and implementation The library is available in Maven Central Repository and its source code is hosted on GitHub: https://github.com/tzok/BioCommons Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals SVIM-asm: Structural variant detection from haploid and diploid genome assemblies

2020 ◽  
Author(s):  
David Heller ◽  
Martin Vingron
Keyword(s):  
Genetic Information ◽  
Source Code ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Diploid Genome ◽  
Insertions And Deletions ◽  
Structural Variant ◽  
Sequencing Technologies ◽  
Variant Detection ◽  
Genome Assemblies

AbstractMotivationWith the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible. These assemblies capture the complete genetic information of both parental haplotypes, increase structural variant (SV) calling sensitivity and enable direct genotyping and phasing of SVs. Yet, existing SV callers are designed for haploid genome assemblies only, do not support genotyping or detect only a limited set of SV classes.ResultsWe introduce our method SVIM-asm for the detection and genotyping of six common classes of SVs from haploid and diploid genome assemblies. Compared against the only other existing SV caller for diploid assemblies, DipCall, SVIM-asm detects more SV classes and reached higher F1 scores for the detection of insertions and deletions on two recently published assemblies of the HG002 individual.Availability and ImplementationSVIM-asm has been implemented in Python and can be easily installed via bioconda. Its source code is available at github.com/eldariont/[email protected] informationSupplementary data are available online.

scholarly journals GalaxyCloudRunner: enhancing scalable computing for Galaxy

2020 ◽  
Author(s):  
N Goonasekera ◽  
A Mahmoud ◽  
J Chilton ◽  
E Afgan
Keyword(s):  
Source Code ◽  
Supplementary Information ◽  
Scalable Computing ◽  
Link Type ◽  
Cloud Providers ◽  
Galaxy Server ◽  
Cloud Resources

AbstractSummaryThe existence of more than 100 public Galaxy servers with service quotas is indicative of the need for an increased availability of compute resources for Galaxy to use. The GalaxyCloudRunner enables a Galaxy server to easily expand its available compute capacity by sending user jobs to cloud resources. User jobs are routed to the acquired resources based on a set of configurable rules and the resources can be dynamically acquired from any of 4 popular cloud providers (AWS, Azure, GCP, or OpenStack) in an automated fashion.Availability and implementationGalaxyCloudRunner is implemented in Python and leverages Docker containers. The source code is MIT licensed and available at https://github.com/cloudve/galaxycloudrunner. The documentation is available at http://gcr.cloudve.org/.ContactEnis Afgan ([email protected])Supplementary informationNone

scholarly journals ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions

2019 ◽  
Vol 35 (22) ◽  
pp. 4754-4756 ◽  
Author(s):  
Egor Dolzhenko ◽  
Viraj Deshpande ◽  
Felix Schlesinger ◽  
Peter Krusche ◽  
Roman Petrovski ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Broad Class ◽  
Source Code ◽  
Computational Method ◽  
Supplementary Information ◽  
Dna Repeats ◽  
Supplementary Data ◽  
Sequence Graph ◽  
Version 2.0 ◽  
Short Tandem

Abstract Summary We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. Availability and implementation ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq

2019 ◽  
Vol 35 (19) ◽  
pp. 3839-3841 ◽  
Author(s):  
Artem Babaian ◽  
I Richard Thompson ◽  
Jake Lever ◽  
Liane Gagnier ◽  
Mohammad M Karimi ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Transposable Element ◽  
Test Data ◽  
Source Code ◽  
Supplementary Information ◽  
Transcriptional Networks ◽  
Supplementary Data ◽  
Rna Seq ◽  
Transcriptional Initiation ◽  
Instruction Manual

Abstract Summary Transposable elements (TEs) influence the evolution of novel transcriptional networks yet the specific and meaningful interpretation of how TE-derived transcriptional initiation contributes to the transcriptome has been marred by computational and methodological deficiencies. We developed LIONS for the analysis of RNA-seq data to specifically detect and quantify TE-initiated transcripts. Availability and implementation Source code, container, test data and instruction manual are freely available at www.github.com/ababaian/LIONS. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals OpenBioLink: a benchmarking framework for large-scale biomedical link prediction

2020 ◽  
Vol 36 (13) ◽  
pp. 4097-4098 ◽  
Author(s):  
Anna Breit ◽  
Simon Ott ◽  
Asan Agibetov ◽  
Matthias Samwald
Keyword(s):  
Link Prediction ◽  
Large Scale ◽  
Source Code ◽  
Machine Learning Algorithms ◽  
Knowledge Networks ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Biomedical Knowledge ◽  
High Quality ◽  
Baseline Evaluation

Abstract Summary Recently, novel machine-learning algorithms have shown potential for predicting undiscovered links in biomedical knowledge networks. However, dedicated benchmarks for measuring algorithmic progress have not yet emerged. With OpenBioLink, we introduce a large-scale, high-quality and highly challenging biomedical link prediction benchmark to transparently and reproducibly evaluate such algorithms. Furthermore, we present preliminary baseline evaluation results. Availability and implementation Source code and data are openly available at https://github.com/OpenBioLink/OpenBioLink. Supplementary information Supplementary data are available at Bioinformatics online.

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