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Clc sequence viewer 7 pdf#
Clc sequence viewer 7 android#

QC-Chain is a package of quality control tools for next generation sequencing (NGS) data, consisting of both raw reads quality evaluation and de novo contamination screening, which could identify all possible contamination sequences.

It is particular designed for 454/Roche data, but can also be used for other types of sequence.

PRINSEQ is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data.

It also includes few other tools, which are helpful in NGS data quality control and analysis. The toolkit comprises user-friendly stand alone 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.

NGS QC Toolkit A toolkit for the quality control (QC) of next generation sequencing (NGS) data.

NGSQC: cross-platform quality analysis pipeline for deep sequencing data.

MultiQC - Aggregate and visualise results from numerous tools (FastQC, HTSeq, RSeQC, Tophat, STAR, others.) across all samples into a single report.

mRIN - Assessing mRNA integrity directly from RNA-Seq data.

Clc sequence viewer 7 pdf#

HTSeq The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.Kraken: A set of tools for quality control and analysis of high-throughput sequence data.fastqp Simple FASTQ quality assessment using Python.FastQC can be run as a stand-alone application or it can be integrated into a larger pipeline solution. Results are presented in HTML permanent reports. This tool provides an overview to inform about problematic areas, summary graphs and tables to rapid assessment of data. Import of data is possible from FastQ files, BAM or SAM format. FastQC is a quality control tool for high-throughput sequence data ( Babraham Institute) and is developed in Java.dupRadar An R package which provides functions for plotting and analyzing the duplication rates dependent on the expression levels.bam-lorenz-coverage A tool that can generate Lorenz plots and Coverage plots, or export these statistics to text files, directly from BAM file(s).AfterQC - Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.Often, is necessary to filter data, removing low quality sequences or bases (trimming), adapters, contaminations, overrepresented sequences or correcting errors to assure a coherent final result. Quality assessment of raw data is the first step of the bioinformatics pipeline of RNA-Seq. Quality control, trimming, error correction and pre-processing of data ssizeRNA Sample Size Calculation for RNA-Seq Experimental Design.Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.

Clc sequence viewer 7 android#

RNAtor: an Android Application to calculate optimal parameters for popular tools and kits available for DNA sequencing projects.

PROPER: PROspective Power Evaluation for RNAseq.

Some important questions like sequencing depth/coverage or how many biological or technical replicates must be carefully considered.

16 Further annotation tools for RNA-Seq dataĭesign is a fundamental step of a particular RNA-Seq experiment.

15 Functional, network and pathway analysis tools.

11.2 Genome-independent ( de novo) assemblers.

7 Fusion genes/chimeras/translocation finders/structural variations.

6.3 Differential isoform/transcript usage.

5 Workbench (analysis pipeline / integrated solutions).

4.2 Evaluation of quantification and differential expression.

4 Normalization, quantitative analysis and differential expression.3.2.2.1 De novo splice aligners that also use annotation optionally.3.2.1 Aligners based on known splice junctions (annotation-guided aligners).2 Quality control, trimming, error correction and pre-processing of data.