Read quality control bioinformatics tools | Next-generation sequencing analysis

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Illumina 33 Roche 13 Life Technologies 9 Pacific Biosciences 6 Oxford Nanopore 4

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Unix/Linux 119 Mac OS 44 Windows 39

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Command line interface 112 Graphical user interface 26 Web user interface 21

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Basic 20 Medium 11 Advanced 113

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None 123 Academic or non-commercial use 10 License purchase required 4

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Python 36 R 31 Perl 30 Java 18 C++ 15 Shell (Bash) 10 Javascript 9 C 7 Cython 2 MATLAB 1 PHP 1 Other 1 Groovy 1

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Bioinformatics 28 BMC bioinformatics 12 BMC genomics 10 bioRxiv 9 Nucleic acids research 7 PLoS one 6 Scientific reports 3 F1000Research 3 Journal of computational biology 3 Gigascience 2 Genomics, proteomics & bioinformatics 2 BMC research notes 2 Cancer informatics 2 Journal of integrative bioinformatics 2 PeerJ 2 IEEE international conference on bioinformatics and biomedicine 1 Genome biology 1 Human mutation 1 Methods in molecular biology 1 BMC medical genomics 1

Funding

National Institutes of Health 6 National Science Foundation 4 Biotechnology and Biological Sciences Research Council 2 German Federal Ministry of Education and Research 1 Conselho Nacional de Desenvolvimento Científico e Tecnológico 1 European Research Council 1 Fondation pour la Recherche Médicale 1 Max Planck Society 1 National Human Genome Research Institute 1 Netherlands Genomics Initiative 1 Swiss National Science Foundation 1 Wellcome Trust 1 Consiglio Nazionale delle Ricerche 1 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior 1 European Molecular Biology Laboratory 1 European Union 1 Institut National du Cancer 1 Graduate School Experimental Plant Sciences 1

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Trim Galore!

(2)

Assists in automating quality, adapter trimming and quality control (QC). Trim Galore! is a wrapper script that provides functionalities to remove biased methylation positions for reduced representation bisulfite sequencing (RRBS) sequence files (for directional, non-directional (or paired-end) sequencing). It can remove sequences if they become too short during the trimming process.

MultiQC

(2)

A tool to create a single report visualizing output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC allows accurate comparison between samples, allowing detection of subtle differences not noticeable when switching between different files. Data visualization aids batch effect detection and minimizes the risk of confounding factors affecting the results of the study.

dDocent

(1)

Offers a platform for population-level analyses. dDocent is an open-source software dedicated to individually barcoded restriction-site associated DNA sequencing (RADseq) data processing. The application employs data reduction techniques and interact with other programs to propose features such as de novo assembly of RAD loci, single nucleotides polymorphisms (SNPs) and indel calling as well as quality trimming or baseline data filtering.

NGS-QC Generator / Next Generation Sequencing Quality Control generator

Assists users to evaluate the quality of ChIP-seq. The NGS-QC database hosts quality scores for over 28,000 datasets, covering a variety of ChIP-sequencing and related assays performed from about 8 species (Homo sapiens: 54%; Mus musculus: 34%; D. melanogaster: 6%). It contains an algorithm designed to: (i) infer a set of global QC indicators (QCis); or to (ii) provide local QCis to judge the robustness of cumulative read counts in a particular region.

HTSeq

A Python library to facilitate the rapid development of scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data, such as genomic coordinates, sequences, sequencing reads, alignments, gene model information and variant calls, and provides data structures that allow for querying via genomic coordinates.

FastQC

(3)

Furnishes functions to control quality for high throughput sequence data. FastQC aims to provide a simple manner to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which users can employ to obtain a quick impression of whether data has any problems of which users should be aware before doing any further analysis.

UEA sRNA toolkit

Allows analysis of high-throughput small RNA data. UEA sRNA toolkit is a suite of interactive sRNA analysis tools, which provides a platform to create workflows for processing small RNA (sRNA) next generation sequencing (NGS) data. The software includes (1) helper tools, (2) computational analysis tools and (3) visualization tools. It permits users to combine workflows and stand-alone tools complemented with visualization features. UEA sRNA toolkit can assist in gaining an understanding of the sRNAome in plants and animals.

BBT / BioBloom tools

Enables creation of filters for a given reference and then categorization of sequences. BBT is a Bloom filter implementation that includes heuristics to control false positives and increase speed. The software was designed for pre-processing and quality check (QC) applications like contamination detection, but it can be suitable for other purposes.

MICRA / Microbial Identification and Characterization through Reads Analysis

Identifies and defines microbes via reads analysis. MICRA employs read mapping methods to make use of the increasing number of sequenced microbial genomes. The working consists in four parts: (1) pre-processing, (2) sequence identification, (3) identification of the closest reference genome and plasmids by the core part and (4) the post-analysis. This pipeline software is available as a download version and as a web interface.

phantompeakqualtools

(1)

Computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays. Phantompeakqualtools can be used to (i) Compute the predominant insert-size (fragment length) based on strand cross-correlation peak; (ii) compute data quality measures based on relative phantom peak; (iii) call peaks and regions for punctate binding datasets

RobiNA

Provides a workflow for RNA-Seq-based differential gene expression (DGE) analysis. RobiNA gathers multiple packages and software with the aim of furnishing a cross-platform processing in four main steps: (i) quality assessment and filtering; (ii) mapping the reads to a user-provided reference genome or transcriptome; (iii) perform the experimental design and (iv) statistical analysis of DGE.

MapSplice

Discovers splice junctions using approximate sequence similarity that is not dependent on features or locations of the splice sites. MapSplice is based on efficient approximate sequence alignment methods combined with a local search. It integrates a rigorous approach to increase specificity of the splice search. This tool is able to detect the exon splice junctions contained in the sampled mRNA transcriptome.

Octopus-toolkit

Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in combining available tools, workflows and training material, as well as providing easy access for experimentalists. It serves as a central hub for programmers, which can easily integrate and deploy their existing or novel tools and workflows.

mistagging

Enables removal of biases and experimental planning for high-throughput sequencing (HTS) platforms. Mistagging can provide more accurate and reproducible HTS data sets, improving the reliability of their interpretations. This tool has the utmost advantage of allowing the establishment of synoptic models towards more comparable diversity analyses.

MOCAT

A software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes.

Hercules

Improves basepair accuracy of long reads. Hercules is an alignment-based hybrid error correction algorithm, using profile hidden Markov models (dubbed profile HMM or pHMM), that corrects erroneous long reads using short but accurate Illumina data. The software models each long and erroneous read as a template profile HMM. It was tested on the following datasets: (i) two BAC clones of complex regions of human chromosome 17, namely, CH17-157L1 and CH17-227A2, and (ii) human brain cerebellum polyA RNA-seq data.

CLC Genomics Workbench

(2)

(1)

Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.

RUbioSeq

Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq is a multi-platform application that uses well established tools to implement pipelines for DNA-seq, CNAseq, bisulfite-seq and ChIP-seq experiments. The software incorporates a graphical user interface (GUI), designed for interdisciplinary research groups where bioinformaticians and biomedical researchers work together. The modular structure permits easy adaptation and extension.

QuickNGS

Aims to reduce the efforts put into basic data processing for next-generation sequencing (NGS). QuickNGS enables data analysis for major applications of NGS in a batch-like operation mode. This pipeline relies on the organization of available metadata in a MySQL database which is used to control the overall workflow composed of specific software applications for different kinds of analysis.

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Bioinformatician 34 Researcher 10 Developer 3 Account Manager 1

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United States of America (the) 9 France 7 India 6 China 5 Korea (the Republic of) 5 Spain 3 Hungary 2 Mexico 2 Belgium 1 Brazil 1 Canada 1 Switzerland 1 Germany 1 United Kingdom of Great Britain and Northern Ireland (the) 1 Norway 1 Pakistan 1 Poland 1 Sweden 1 Turkey 1 Taiwan (Province of China) 1

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Python 31 R 27 Shell (Bash) 14 Perl 13 C++ 9 Java 8 Javascript 6 MATLAB 6 PHP 6 C 4 Other 2 Objective-C 1 Visual Basic 1 C# 1 COBOL 1

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1 - 20 of 662 results

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Application

RNA-seq analysis 410 Metatranscriptomic sequencing analysis 346 sRNA-seq analysis 199 De novo sequencing analysis 183 WGS analysis 158 WES analysis 114 scRNA-seq analysis 98 Metagenomic sequencing analysis 92 GBS analysis 77 Ribo-seq analysis 71 ChIP-seq analysis 61 CAGE analysis 58 DNase-seq analysis 50 CLIP-seq analysis 44 Rep-seq analysis 27 BS-seq analysis 11 RAD-seq analysis 4 Hi-C analysis 2 Amplicon sequencing analysis 2 Transcription analysis 1

Tool

FastQC 423 TopHat 187 FASTX-Toolkit 120 Cufflinks 119 HTSeq 103 Bowtie 102 Bowtie2 97 Trimmomatic 93 BWA 78 SAMtools 77 cutadapt 64 edgeR 49 Trinity 47 DESeq2 45 DESeq 43 BCL2FASTQ Conversion Software 41 Picard 39 STAR 38 PRINSEQ 37 GATK 33

Technology

Illumina 541 Roche 519 Pacific Biosciences 430 Oxford Nanopore 79 Life Technologies 52

Operating System

Unix/Linux 662 Mac OS 617 Windows 572

Interface

Command line interface 662 Graphical user interface 475 Web user interface 193 Application programming interface 11

Computer Skill

Basic 193 Medium 76 Advanced 662

Restriction to use

None 661 Academic or non-commercial use 103 License purchase required 77

Programming Language

Java 500 C++ 484 C 377 Python 317 R 274 Perl 254 Cython 104 Javascript 83 Shell (Bash) 75 MATLAB 6 PHP 3 Ruby 3

Disease

Neoplasms 58 Infection 40 Brain Diseases 27 Neurologic Manifestations 21 Inflammation 18 Sexually Transmitted Diseases, Viral 18 Retroviridae Infections 17 HIV Infections 17 Breast Diseases 16 Digestive System Neoplasms 15 Intestinal Diseases 15 Breast Neoplasms 14 Leukemia 12 Neoplasms, Glandular and Epithelial 11 Disease 10 Urogenital Neoplasms 10 Euglenozoa Infections 9 Neoplastic Processes 7 Urologic Diseases 7 Kidney Diseases 6

Taxonomy

Homo sapiens 206 Mus musculus 63 Escherichia coli 28 Arabidopsis thaliana 26 Bos taurus 25 Drosophila melanogaster 20 Saccharomyces cerevisiae 17 Caenorhabditis elegans 16 Oryza sativa 12 Zea mays 11 Bacteria 10 Rattus norvegicus 9 Danio rerio 9 Gallus gallus 7 Sus scrofa 7 Viruses 6 Triticum aestivum 6 Equus caballus 6 Human poliovirus 1 Mahoney 5 Toxoplasma gondii 5

Chemical

Nucleotides 24 Hydrocarbons, Cyclic 24 Heterocyclic Compounds, 2-Ring 22 Metals, Heavy 21 Transition Elements 20 Oxygen 17 Monosaccharides 16 Carbon 16 Chalcogens 15 Amino Acids 15 Steroids 14 Ribonucleotides 10 Pyrimidines 10 Nitrogen 10 Disaccharides 9 Hydrocarbons, Acyclic 9 Terpenes 9 Purine Nucleotides 8 Oligosaccharides 8 Acids, Carbocyclic 7

Journal

PLoS one 121 Scientific reports 90 BMC genomics 55 Genome announcements 39 Nature communications 30 Frontiers in plant science 24 Nucleic acids research 19 PLoS genetics 17 Oncotarget 17 eLife 16 Frontiers in microbiology 13 Genome biology 12 Genome biology and evolution 12 BMC plant biology 8 Frontiers in genetics 7 PLoS pathogens 7 Genomics data 7 Microbiome 6 mBio 6 PLoS neglected tropical diseases 6

Funding

Bill and Melinda Gates Foundation 1 National Institutes of Health 1 National Natural Science Foundation of China 1 National Science Foundation 1

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B cell activation and plasma cell differentiation are inhibited by de novo DNA methylation

Tools (3): FastQC, Bismark, SAMtools

Topics (1): BS-seq analysis

Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells

Tools (7): FastQC, cutadapt, BWA, SAMtools, Picard, GATK, SnpEff

Topics (1): WGS analysis

Waveband specific transcriptional control of select genetic pathways in vertebrate skin (Xiphophorus maculatus)

Tools (3): FastQC, GSNAP, edgeR

Topics (5): RNA-seq analysis, CAGE analysis, Metatranscriptomic sequencing analysis, Xiphophorus maculatus, Necrosis

A genome-wide assessment of conserved SNP alleles reveals a panel of regulatory SNPs relevant to the peripheral nerve

Tools (7): FastQC, TagDust, BWA, Paraclu, STAR, HTSeq, DESeq2

Topics (7): CAGE analysis, RNA-seq analysis, scRNA-seq analysis, Metatranscriptomic sequencing analysis, Homo sapiens, Mus musculus, Caenorhabditis elegans

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

Tools (4): Bowtie, RSEM, FastQC, CLC Genomics Workbench

Topics (8): Metatranscriptomic sequencing analysis, Zymomonas mobilis, Seizures, Neurologic Manifestations, Nucleotides, Chalcogens, Oxygen, Monosaccharides

Regulation Mechanism Mediated by Trans-Encoded sRNA Nc117 in Short Chain Alcohols Tolerance in Synechocystis sp. PCC 6803

Tools (4): NGS QC Toolkit, HTSeq, DESeq2, GOseq

Topics (7): RNA-seq analysis, Synechocystis sp. PCC 6803, Ethanol, Alcohols, Nucleotides, Fatty Alcohols, Butanols

C/EBPβ enhances platinum resistance of ovarian cancer cells by reprogramming H3K79 methylation

Tools (6): FastQC, TopHat, Cufflinks, HTSeq, DESeq2, gplots

Topics (9): RNA-seq analysis, Homo sapiens, Neoplasms, Ovarian Diseases, Genital Diseases, Female, Ovarian Neoplasms, Endocrine Gland Neoplasms, Transition Elements, Metals, Heavy

Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods

Tools (7): FastQC, BWA, QualiMap, Picard, BEDTools, GATK, VCFtools

Topics (4): WGS analysis, WES analysis, Neoplasms, Genetic Diseases, Inborn

Viral proteins as a potential driver of histone depletion in dinoflagellates

Tools (3): FastQC, BWA, SAMtools

Topics (4): GBS analysis, WGS analysis, WES analysis, Saccharomyces cerevisiae

Intact interleukin-10 receptor signaling protects from hippocampal damage elicited by experimental neurotropic virus infection of SJL mice

Tools (3): FastQC, TopHat, HTSeq

Topics (16): RNA-seq analysis, Metatranscriptomic sequencing analysis, scRNA-seq analysis, sRNA-seq analysis, Mus musculus, Human poliovirus 1 Mahoney, Viruses, Craniocerebral Trauma, Brain Diseases, Encephalomyelitis, Central Nervous System Infections, Nerve Degeneration, Alcohol-Related Disorders, Brain Diseases, Metabolic, Malnutrition, Brain Diseases

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing

Tools (4): FastQC, Trinity, CD-HIT, BLASTX

Topics (2): RNA-seq analysis, Metatranscriptomic sequencing analysis

A Comparative Genomic Analysis Provides Novel Insights Into the Ecological Success of the Monophasic Salmonella Serovar 4,[5],12:i:-

Tools (3): FastQC, Trimmomatic, Velvet

Topics (10): De novo sequencing analysis, GBS analysis, Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344, Sus scrofa, Transition Elements, Metals, Heavy, Transition Elements, Metals, Heavy, Transition Elements, Metals, Heavy

Transcriptomic Analysis of Flower Bud Differentiation in Magnolia sinostellata

Tools (6): FastQC, Trinity, BLASTX, RSEM, DESeq, TBtools

Topics (1): RNA-seq analysis

Helicase-like transcription factor expression is associated with a poor prognosis in Non-Small-Cell Lung Cancer (NSCLC)

Tools (3): Cufflinks, FastQC, RSeQC

Topics (13): De novo sequencing analysis, Homo sapiens, Neoplasms, Glandular and Epithelial, Lung Neoplasms, Thoracic Neoplasms, Neoplasms, Glandular and Epithelial, Lung Neoplasms, Thoracic Neoplasms, Neoplasms, Heredodegenerative Disorders, Nervous System, Spinal Cord Diseases, Dyskinesias, Brain Diseases

Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle

Tools (5): NGS QC Toolkit, TopHat, Cufflinks, BiNGO, Cytoscape

Topics (4): RNA-seq analysis, Fungi, Homo sapiens, Mycoses

Gene expression and ultrastructure of meso‐ and thermophilic methanotrophic consortia

Tools (3): FastQC, BBMap, BEDTools

Topics (12): Ribo-seq analysis, RNA-seq analysis, Metatranscriptomic sequencing analysis, scRNA-seq analysis, sRNA-seq analysis, Escherichia coli, Bacteria, Heterocyclic Compounds, 4 or More Rings, Porphyrins, Azoles, Tetrapyrroles, Hydrocarbons, Acyclic

Characterizing Phage Genomes for Therapeutic Applications

Tools (3): MegaBLAST, FaQCs, PhageTerm

Topics (4): Metagenomic sequencing analysis, De novo sequencing analysis, Filamentous phage, Bacterial Infections

Hidden genomic MHC disparity between HLA-matched sibling pairs in hematopoietic stem cell transplantation

Tools (3): GATK, FastQC, cutadapt

Topics (4): WES analysis, WGS analysis, Homo sapiens, Nucleotides

Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites

Tools (4): FastQC, Trimmomatic, Bowtie2, SAMtools

Topics (6): GBS analysis, WGS analysis, WES analysis, Homo sapiens, Rattus norvegicus, Hydrocarbons, Halogenated

The influence of transcript assembly on the proteogenomics discovery of microproteins

Tools (3): BCL2FASTQ Conversion Software, FastQC, STAR

Topics (6): Ribo-seq analysis, scRNA-seq analysis, RNA-seq analysis, Metatranscriptomic sequencing analysis, sRNA-seq analysis, Homo sapiens

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