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1 - 50 of 111 results

1 - 50 of 111 results

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.

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.

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.

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.

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.

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.

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.

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.

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.

Verifies sample identities from FASTQ, BAM or VCF files. NGSCheckMate uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms (SNPs), considering depth-dependent behavior of similarity metrics for identical and unrelated samples. It is effective for a variety of data types, including exome sequencing, whole-genome sequencing, RNAseq, ChIP-seq, targeted sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth. The tool can be used as a quality control step in next-generation sequencing (NGS) studies.

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.

CLC bio / CLC Genomics Workbench

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.

Assists users in manipulating high-throughput sequencing (HTS) data and formats. Picard is a Java toolkit that provides a set of command line scripts. It comprises Java-based utilities that manipulate SAM files, and a Java API for creating new programs that reads and writes SAM files. Both SAM text format and SAM binary (BAM) format are supported. It also works with next generation sequencing (NGS).

A package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead extends Bioconductor with tools useful in the initial stages of short-read DNA sequence analysis. Main functionalities include data input, quality assessment, data transformation and access to downstream analysis opportunities. It is an important gateway to use of Bioconductor for processing high-throughput DNA sequence data. ShortRead data structures allow convenient manipulation of data, such as filtering reads based on sequence characteristics.

Displays statistics of large sequence files from next-generation sequencing (NGS) projects. SAMStat is a program which plots nucleotide over-representation and other statistics in mapped and unmapped reads. The software can be used to verify individual processing steps in large analysis pipelines. Specific applications include the verification and quality control of processing pipelines, the tracking of data quality over time and the visualization of data properties derived from new protocols.

Allows users simultaneously perform mRNA and miRNA expression analysis. wapRNA is a web application that includes major processes for the next-generation mRNA or miRNA data analysis, including preprocessing raw sequenced reads, mapping tags to reference sequences, gene expression annotation, and other downstream functional analysis such as detecting differentially expressed genes, Gene Ontology and KEGG pathway analysis for RNA, novel miRNA predication and miRNA target prediction. Executable packages are available for users to build their pipeline locally.

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops. oneChannelGUI can be used for quality control, normalization, filtering, statistical validation and data mining for single channel microarrays. It consists of a didactical tool that can be employed to introduce scientists to the utilization and interpretation of microarray data. This tool serves in the investigation of microarray experiments based on the consolidated 3’ Affymetrix expression arrays.

KAT / K-mer Analysis Toolkit

A user-friendly, extendible and scalable toolkit for rapidly counting, comparing and analysing k-mers from various data sources. The tools in KAT assist the user with a wide range of tasks including error profiling, assessing sequencing bias and identifying contaminants and de novo genome assembly QC and validation. KAT is a C++11 application containing multiple tools, each of which exploits multi-core machines via multi-threading where possible. Core functionality is contained in a library designed to promote rapid development of new tools.

Allows users to characterize and quantify the set of all RNA molecules produced in cells. RseqFlow contains several modules that include: mapping reads to genome and transcriptome references, performing quality control (QC) of sequencing data, generating files for visualizing signal tracks based on the mapping results, calculating gene expression levels, identifying differentially expressed genes, calling coding single nucleotide polymorphisms (SNPs) and producing MRF and BAM files.

aRNApipe / automated RNA-seq pipeline

Analyzes single-end and stranded or unstranded paired-end RNA-seq data. aRNApipe focuses on high performance computing (HPC) environments and the independent designation of computational resources at each stage allowing optimization of HPC resources. It is highly flexible because its project configuration and management options. This tool can be adapted to changes in the current applications and the addition of new functionalities. It allows users to complete primary RNA-seq analysis.

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal experiments. NGS-Bits is separate into four steps: (1) gather information from raw reads, (2) map reads, (3) extract variant lists, and (4) combine result from precedent steps to then add quality control (QC) metrics for tumor-normal experiments. This tool includes all stages of single-sample NGS data analysis and adds special QC metrics for DNA sequencing of tumor-normal pairs.

Allows to develop tailored workflows for the analysis of whole-exome (WES), whole-genome (WGS), and transcriptome (RNA-seq) sequencing data. NGS-pipe is an automated framework for the design of pipelines for the analysis of large-scale sequencing data, such as cancer genomics data. It provides building blocks to execute state-of-the-art tools, as well as appropriate error handling. It also overcome the common lack of automated procedures to ensure reproducibility.

AlmostSignificant

An open-source platform for aggregating multiple sources of quality metrics as well as meta-data associated with DNA sequencing runs from Illumina NextSeq and HiSeq machines. AlmostSignificant is a graphical platform to streamline the quality control of DNA sequencing data, to collect and store these data for future reference and to collect extra meta-data associated with the sequencing runs to check for errors and monitor the volume of data produced by the associated machines.

Permits to process and analyze the raw files generated with the Spatial Transcriptomics (ST) method. ST Pipeline enables demultiplexing of spatially-resolved RNA-seq data and robust quality filtering and identification of unique molecules. It is highly customizable with numerous parameter settings. The tool is more robust, efficient and scales better to arrays with higher density. It filters data, aligns it to a genome, annotates it to a reference, demultiplexes by array coordinates and then aggregates by counts that are not duplicates using the Unique Molecular Identifiers.

Facilitates quality control (QC) of FASTQ files. FQC combines a command line interface (CLI) depending on FastQC for processing FASTQ files, and a frontend website for plotting, styling and interactivity. The CLI wraps FastQC and builds the website with default QC metrics upon which one can expand without additional programming. The CLI and dashboard lower the threshold of performing and following up on quality issues that may be apparent upon visual inspection and it promotes evidence-based protocol changes in sequencing facilities to generate better quality data.

Processes raw reads to count tables for RNA-seq data using Unique Molecular Identifiers (UMIs). zUMIs is a pipeline applicable for most experimental designs of RNA-seq data, such as single-nuclei sequencing techniques. This method allows for down sampling of reads before summarizing UMIs per feature, which is recommended for cases of highly different read numbers per sample. zUMIs is flexible with respect to the length and sequences of the barcodes (BCs) and UMIs, making it compatible with a large number of protocols.

A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information). The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ and many many others.

Designed for mRNA, miRNA and circRNA identification and differential expression analysis, applicable to any sequenced organism. miARma-Seq is presented as a stand-alone tool that provides different well-established softwares at ease of installation process. It can analyse a large number of samples due to its multithread design. During the whole analysis miARma-Seq performs several quality control analysis creating quality reports for an easy evaluation of the data.

Analyzes the structure and functions of active microbial communities using the power of multi-threading computers. MetaTrans is designed to perform two types of RNA-Seq analyses: taxonomic and gene expression. It performs quality-control assessment, rRNA removal, maps reads against functional databases and also handles differential gene expression analysis. Its efficacy was validated by analyzing data from synthetic mock communities, data from a previous study and data generated from twelve human fecal samples.

A toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly standalone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis.

SUGAR / SUbtile-based GUI-Assisted Refiner

Evaluates quality and quality-based cleaning of full HiSeq and MiSeq data. SUGAR can produce high-resolution quality heatmaps of the flowcell to display possible signals of technical errors during the sequencing. This software intends to curtail technical problems in sequence read mapping and enhance subsequent variant analysis that require high-quality sequence data and mapping results.

A-GAME / A GAlaxy suite for functional MEtagenomics

Incorporates tools and workflows for the analysis of environmental DNA (eDNA) sequence data. A-GAME is a general bioinformatics workflow management system implemented within Galaxy. The software contains pre-designed workflows that utilize standard tools for data pre-processing, sequence assembly and annotation; as well as custom utilities dedicated to the analysis of functional metagenomics data. It allows the incorporation of most widely used bioinformatics tools. A-GAME can be used to build and customize bioinformatics workflows.

RAP / RNA-seq Analysis Pipeline

Allows users to analyze sequencing data in multiple steps. The RAP purpose is to investigate the complex transcriptional landscape of eukaryotic transcriptomes through a computationally optimized RNA-Seq data analysis. Users can perform a complete RNA-Seq analysis without any specific technical competence. It offers a web interface and provides different types of results which consist of several tabular and graphical representations.

Allows analysis of next-generation sequencing datasets. Kraken is a suite of tools that encompasses adapter contaminant detection and removal, and cleaning of low-complexity and low-quality sequence tracts and other contaminants arising from sample preparation. The software can handle multiplexed data, recognize common read geometries, produce reports, plots and summary statistics, and process several FASTQ files in parallel.

A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and a careful selection of previously published algorithmic approaches to build fully automated data analysis workflows. QuickNGS considerably reduces the barriers that still limit the usability of the powerful NGS technology and finally decreases the time to be spent before proceeding to further downstream analysis and interpretation of the data.

CoVaCS / Consensus Variant Calling System

Enables genotyping and variant annotation of resequencing data produced by second generation next generation sequencing (NGS) technologies. CoVaCS is an automated system that provides tools for variant calling and annotation along with a pipeline for the analysis of whole genome shotgun (WGS), whole exome sequencing (WES) and targeted resequencing data (TGS). The software allows non-specialists to perform all steps from quality trimming to variant annotation.

Provides a solution for RNA-Seq data quality control (QC). RNA-QC-Chain includes three related functional components, called Parallel-QC, rRNA-filter and SAM-stats. The software performs sequencing quality trimming for raw read, automatic contamination identification and filtering, and alignments statistics reporting. It can filter out the poor-quality reads and contaminations and generate the ready-to-use data for downstream analysis.

Includes three types of workflows for different tasks. RNA-seq portal permits users to perform computing and analysis, including sequence quality control, read-mapping, transcriptome assembly, reconstruction and differential analysis. All these workflows support multiple samples and multiples groups of samples and perform differential analysis between groups in a single workflow job submission. This web portal offers bioinformatics software, workflows, computation and reference data and a platform to study complex RNA-seq data analysis for agricultural animal species.

Allows analyses of high-throughput small RNA (sRNA) sequence data in model and non-model plants, from raw data to identified and annotated conserved and novel sequences. miRPursuit is a pipeline performing a series of sRNA analyses. The software minimizes the need to perform manual repetitive tasks allowing to run several libraries in parallel, for comparing differences in sRNA read accumulation among sRNA libraries. It can directly analyze the sRNA sequencing raw data from any sequencer.

A user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. SolexaQA contains associated software to trim sequences dynamically using the quality scores of bases within individual reads. It produces standardized outputs within minutes, thus facilitating ready comparison between flow cell lanes and machine runs, as well as providing immediate diagnostic information to guide the manipulation of sequence data for downstream analyses.

Processes scripts generated by next-generation sequencing (NGS) platforms (Roche 454, Illumina HiSeq2000, Illumina MisEQ). mubiomics provides quality control (QC), read demultiplexing and microbiome characterization scripts compatible with several tools like usearch, pplacer, RDP classifier. The QC and demultiplexing methods of this software are based on the QIIME tool.

OncoRep / Oncogenomics Report

A fully automated RNA-Seq based report for patients with (breast) cancer, which includes molecular classification, detection of altered genes, detection of altered pathways, identification of gene fusion events, identification of clinical actionable mutations (in coding regions) and identification of treatable target structures. Furthermore, OncoRep reports suitable drugs based on identified actionable targets, which can be considered in the treatment decision making process.

Performs tasks required for the analysis of mapped RNA-Seq reads. S-MART performs different categories of tasks: (i) it can filter and select the data of most interest, cluster the information to acquire a bird’s eye view, or convert the data from one file format to another; (ii) it can produce high-quality graphs to visualize some aspects of the information from the reads, or plot some general distributions; and (iii) it can discriminate the differentially expressed genes.

Evaluates an alignment for mismatches. Mmfind offers a strategy for the identification, evaluation and verification of reliable polymorphisms between conventional Sanger ESTs and 454-FLX ESTs, by making use of the quality values for both sequence types. It explores the potential of combining existing, reliable and high-quality sequence datasets with the power of cost-effective, high-throughput sequence generation.

CorQ / CORrection through Quality

Assists in correcting for homopolymer and non-homopolymer insertion and deletion errors. CorQ is an error correction algorithm that uses a set of sequences and associated quality files as a starting point for error correction. It uses the filtered sequence alignment file to correct indel and miscall errors. It also creates an annotation file that tracks changes made to each corrected read.

FaQCs / FastQ Quality Control Software

A software package that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

Processes FASTQ files in batches. AfterQC is an application with rich quality control, data filtering, error profiling and correction functions for next generation sequencing (NGS) data. This method addresses major practical sequencing data quality control and filtering problems. It automatically detects and cuts adapters for pair-end data, with no need of adapter sequence input. It also provides functions like automatic trimming and overlapping analysis.

HTQC / High-Throughput Quality Control

A toolkit named for sequence reads quality control, which consists of six programs for reads quality assessment, reads filtration and generation of graphic reports. The HTQC toolkit can generate reads quality assessment faster than existing tools, providing guidance for reads filtration utilities that allow users to choose different strategies to remove low quality reads.

TRAPLINE / Transparent Reproducible and Automated PipeLINE

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides researchers through the NGS data analysis process in a transparent and automated state-of-the-art pipeline. It can detect protein-protein interactions (PPIs), miRNA targets and alternatively splicing variants or promoter enriched sites. This tool includes different modules for several functions: (1) it scans the list of differentially expressed genes; (2) it includes modules for miRNA target prediction; and (3) a module is implemented to identify verified interactions between proteins of significantly upregulated and downregulated mRNAs.

Masks substitutes low quality base calls with ‘N’s (undetermined bases) in Next generation sequencing (NGS) data. subN is an effective preprocessing method for NGS data analysis since masking reduces the false-positive rate in single nucleotide polymorphism (SNP) calling without sacrificing the false-negative rate. SubN program is available for public, simple and small (less than 200 lines), and easy to use.

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QuaCRS / Quality Control for RNA-Seq

Serves for RNA-seq quality control (QC). QuaCRS assists users in identification of quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies. This application contains and executes three tools: FastQC, RNA-SeQC and RSeQC. These modules supply a complete view of sample data. It also includes a database allowing users to display the resulting metrics.

1 - 32 of 32 results

1 - 32 of 32 results

VDJtools tcR COV2HTML

Bioinformatician OmicX

PhD ès Neurosciences, I worked 8 years on the brain and its diseases. I then specialized in bioinformatics (NGS, epigenetics) and worked in CEA and GENETHON before to join OMICX and help OMICtools community.

aCNViewer MEDOC Bowtie

Big data scientist National Institute of Plant Genome Research

Research Interests Gene fusion detection in Plants Fusion transcripts (i.e., chimeric RNAs) resulting from gene fusions are well known in case of human. But, in plants, this phenomenon is not yet explored. We are planning to discover the fusion transcripts/gene fusions in different type of plants by using RNA-Seq datasets. Further, we are planning to understand the mechanism of gene fusion formation and significance of fusions in plants. Whole genome and transcriptome sequencing data analysis of Plants In this era of Next Generation Sequencing (NGS), there is huge amount of sequencing data available in the public domain. Any novel finding from these available datasets is major challenge for a computational biologist. We are interested in the analysis of whole genome and transcriptome sequencing data of different plants to fetch out the useful information from those datasets, with the help of bioinformatics tools. Currently, we are planning to study the gene clusters of secondary metabolite pathways in different plants. Development of webservers, databases and computational pipelines for plant research Development of database is necessary to compile and share the information with scientific community. We are dedicated to develop useful databases and webserver for plant research. Another area of interest is to develop automated pipelines and tools for the analysis of high throughput genomics data, generated by NGS technologies. Professional & Academic Background Staff Scientist II (May 2017- present): National Institute of Plant Genome Research (NIPGR), New Delhi, India Postdoctoral Research Associate (2015-2017): University Of Virginia, Charlottesville, VA, USA Research Scientist (2014-2015): Sir Ganga Ram Hospital, New Delhi, India PhD Bioinformatics (2009-2014): Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh under Jawaharlal Nehru University (JNU), New Delhi, India M.Sc. Life Sciences (2007-2009): Jawaharlal Nehru University (JNU), New Delhi, India B.Sc. Biotechnology (2004-2007): Jamia Millia Islamia (JMI), New Delhi, India Awards and Fellowships Junior and Senior Research Fellowship (2009-2014): Council of Scientific and Industrial Research (CSIR), New Delhi, India GATE (Graduate Aptitude Test in Engineering): Qualified in years 2008 and 2009 Scientific Contributions/ Recognitions Associate editor: Journal of Translational Medicine. Editorial Board Member of Journal: Theoretical Biology and Medical Modelling. Reviewer: PloS One, BMC Genomics, BMC Bioinformatics, BMC Biology, BMC Biotechnology, Frontiers in Physiology and several other journals. Web Resources/ Databases (Developed/ Contributed) A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer (http://www.imtech.res.in/raghava/cancertope/) GenomeABC: A webserver for benchmarking of genome assemblers. (http://crdd.osdd.net/raghava/genomeabc/). Genomics web portal page. (http://crdd.osdd.net/raghava/genomesrs/). Map/Alignment module of CancerDr: Cancer Drug Resistance Database. (http://crdd.osdd.net/raghava/cancerdr/). Short reads and contigs alignment module of PCMDB: Pancreatic cancer methylation database. (http://crdd.osdd.net/raghava/pcmdb/). Burkholderia sp. SJ98 database. (http://crdd.osdd.net/raghava/genomesrs/burkholderia/). Rhodococcus imtechensis RKJ300 database. (http://crdd.osdd.net/raghava/genomesrs/rkj300/). Genotrick: A pipeline for whole genome assembly and annotation of Genomes (http://crdd.osdd.net/raghava/genomesrs/genotrick/) Development of Debian packages in OSDDlinux: A Customized Operating System for Drug Discovery. (http://osddlinux.osdd.net/). A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. (http://crdd.osdd.net/raghava/mtbveb/).

FusionFinder comrad

Vijay Lakhujani

Bioinformatician | Avid Learner | Programmer Xcelris Labs

☛ I am a DBT Certified bioinformatician (BINC, Govt. Of India) with deep interest in Genomics and next generation sequencing technologies. I have enjoyed my industry experience of 6.5+ years working on design, implementation and analysis of microarray data and high-throughput NGS data. ☛ I love the idea of automation and my passion for programming has motivated me to learn some of the top-notch programming languages like PERL, Python, bash and R. I have developed several programs required to analyze, manipulate or automate key steps in sequencing data analysis. Programming is so much fun! ☛ I am an avid learner and I often try to engage myself in online courses because I strongly believe that in a quickly evolving domain like bioinformatics, the only way to keep up the pace with is to keep learning, both within and outside the job hours. ☛ I support the concept of “open-source” and try to share as much as knowledge regarding bioinformatics and its scope with students. I have been formally certified as “lecturer” (CSIR-NET-JRF+LS, Govt. of India) and involved in providing bioinformatics knowledge sharing sessions and cross functional trainings to technical teams and graduate students. ☛ You can connect with me via gmail, LinkedIn or over a call to discuss ideas or if you need any guidance. Here are my contact details. ✉ [email protected] ✆ +91 966 22 55 385 ▣ Linkedin: https://in.linkedin.com/in/lakhujanivijay ❝Everybody in this country should learn to program a computer, because it teaches you how to think❞ ✍ Steve Jobs

Agilent CytoGenomics software FastQC PHASTER

Bioinformatician Purdue University

Bismark

Researching the microbiology of anaerobic digesters fed with lignocellulosic substrates University of Szeged

Parallel-META phyloseq mothur

Master Korea Advanced Institute of Science and Technology

SAMtools Sickle Zika-RNAseq-Pipeline

Mahantesh Biradar

‎Graduate PhD researcher focusing on Cardiovascular Epidemiology & Social Media Enthusiast Research Stash

I'm a Graduate PhD researcher in the area of Biomedical Science and focussing on the Pharmacogenomics/Pharmacogenomics of Diabetes and related complications

Head of Facility, Genomics Applications Development, National Genomics Infrastructure Science for Life Laboratory

Bioinformatician working with next generation sequencing data.

MultiQC

PhD Student Institute of Life Sciences

Working on Immunology and Systems Biology.

EuMicrobedbLite Bowtie GATK

Emeline Duquenne

Biocurator OmicX

miRNATIP LMAT HebbPlot

INSERM U1065, C3M University of Nice Sophia-Antipolis, France French Institute of Health and Medical Research

PIPE-chipSAD

Rodrigo Bacigalupe

Scientist Flanders Institute for Biotechnology

Antoine Rousselin

Ingénieur d'étude Centre Franois Baclesse

ONCOCNV CNVkit CNV-seq

Elhadji Thioune

Biocurator OmicX

Bowtie SAMtools BWA

cell biology Guangzhou Institutes of Biomedicine and Health

deepTools SCDE Glbase

Dr Wirth Roland

Biotechnologist University of Szeged

metaWRAP MEGAN GraPhlAn

olga Adame Guerero

Student Universidad Autónoma de Guerrero

Bioinformatics Seoul National University

miARma-Seq RSEM EBSeq

Bioinformatics Chinese Academy of Sciences

German Uritskiy

Microbial ecologist Johns Hopkins University

metaWRAP

Leonardo Normando

Microbial Ecology Universidade Federal do Ceará

QIIME Trim Galore! FASTX-Toolkit

Bioinfomagician Dankook University

Octopus-toolkit

Bioinformatic Programmer II University of California, San Francisco

zUMIs CEMiTool SinQC

Graduate Research Assistant South Dakota State University

IRIS GeneQC ViDGER

researcher XenoGene

Kraken Centrifuge Kraken

I am an Electrical Engineer and Developer University of Engineering and Technology Lahore

SNPSVM GATK SAMtools

Rinaldo Catta-Preta

Graduate Student Researcher University of California Davis Medical Center

DeepEnhancer Spectacle BWA

Adrien Taudiere

Ecology and metagenomics Centre d'Ecologie Fonctionnelle et Evolutive

Professional website: http://adrientaudiere.github.io/

Sickle QIIME edgeR

wapRNA Tuxedo ARCHS4

Rupak Dey Sarkar

Post graduate student Presidency University

Bowtie Salmon SAMtools

Bioinformatics Software Developer and Medical Doctor D-BSSE - ETHZ/Basel

SAMtools BWA V-pipe

Read quality assessment software tools | High-throughput sequencing data analysis

Next-generation sequencing (NGS) technologies have been widely used in life sciences. However, several kinds of sequencing artifacts, including low-quality reads and contaminating reads, were found to be quite common in raw sequencing data, which compromise downstream analysis. Therefore, quality control (QC) is essential for raw NGS data.

Source text:
(Zhou et al., 2013) QC-Chain: fast and holistic quality control method for next-generation sequencing data. PLoS One.

Parent categories

CLIP-seq analysis ChIP-seq analysis Metagenomic sequencing analysis RNA-seq analysis sRNA-seq analysis De novo sequencing analysis GBS analysis BS-seq analysis Metatranscriptomic sequencing analysis Rep-seq analysis

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