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Read quality control software tools | Whole-genome 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…
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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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QualiMap
Desktop

QualiMap

A Java application that supports user-friendly quality control of mapping data,…

A Java application that supports user-friendly quality control of mapping data, by considering sequence features and their genomic properties. Qualimap takes sequence alignment data and provides…

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Pyrotools
Desktop

Pyrotools

Represents the consensus sequences in a region of interest (ROI). Pyrotools is…

Represents the consensus sequences in a region of interest (ROI). Pyrotools is based on the graph technique that resembles the partial order graph or variant graph. It can model error patterns in the…

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SeqControl
Desktop

SeqControl

A set of Perl and R scripts designed to assess the quality of sequencing data…

A set of Perl and R scripts designed to assess the quality of sequencing data using multiple quality metrics. The pipeline takes one or more sorted BAM files as input, and outputs multiple files…

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ShortRead
Desktop

ShortRead

A package for input, quality assessment, manipulation and output of…

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…

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SRMA
Desktop

SRMA Short Read Micro re-Aligner

A post-alignment micro re-aligner for next-generation high throughput…

A post-alignment micro re-aligner for next-generation high throughput sequencing data.

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gPCA
Desktop

gPCA guided Principal Component Analysis

Provides guided principal components (PCA) analysis for the detection of batch…

Provides guided principal components (PCA) analysis for the detection of batch effects in high-throughput data. gPCA provides a statistic method particularly useful to test whether batch effects…

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NGS QC Toolkit
Desktop

NGS QC Toolkit

A toolkit for the quality control (QC) of next generation sequencing (NGS)…

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…

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SolexaQA
Desktop

SolexaQA

A user-friendly software package designed to generate detailed statistics and…

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…

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discovering-cse
Desktop

discovering-cse

A statistically rigorous framework for the discovery of motifs that induces…

A statistically rigorous framework for the discovery of motifs that induces sequencing errors. Discovering-cse detects the motifs and aggregates information at matching positions to identify…

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SAMStat
Desktop

SAMStat

Displays statistics of large sequence files from next-generation sequencing…

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…

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Genotypeeval
Desktop

Genotypeeval

Provides method to identify and mitigate batch effects in whole genome…

Provides method to identify and mitigate batch effects in whole genome sequencing (WGS) data. Genotypeeval can process genotypes stored in gVCF or VCF files and computes 46 metrics selected to assess…

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FQC
Desktop

FQC

Facilitates quality control (QC) of FASTQ files. FQC combines a command line…

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…

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Pheniqs
Desktop

Pheniqs PHilology ENcoder wIth Quality Statistics

Demultiplexes sequence and analyzes quality. Pheniqs introduces a…

Demultiplexes sequence and analyzes quality. Pheniqs introduces a Phred-adjusted maximum likelihood decoder that consults base calling quality scores and estimates the probability of a barcode…

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NGSCheckMate
Desktop

NGSCheckMate

Verifies sample identities from FASTQ, BAM or VCF files. NGSCheckMate uses a…

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…

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ClinQC
Desktop

ClinQC

An integrated, automated, flexible and user-friendly tool for quality control…

An integrated, automated, flexible and user-friendly tool for quality control in clinical research. It supports three major NGS sequencing technologies including Illumina, 454 and Ion Torrent along…

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MuffinInfo
Web
Desktop

MuffinInfo

A FastQ/Fasta/SAM information extractor implemented in HTML5 capable of…

A FastQ/Fasta/SAM information extractor implemented in HTML5 capable of offering insights into next-generation sequencing (NGS) data. MuffinInfo can run on any software or hardware environment, in…

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Kraken
Desktop

Kraken

A set of tools for quality control and analysis of high-throughput sequence…

A set of tools for quality control and analysis of high-throughput sequence data.

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ReQON
Desktop

ReQON Recalibrating Quality Of Nucleotides

Recalibrates the base quality scores from an input BAM file of aligned…

Recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration.…

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KAT
Desktop

KAT K-mer Analysis Toolkit

A user-friendly, extendible and scalable toolkit for rapidly counting,…

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…

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MultiQC
Desktop

MultiQC

A tool to create a single report visualizing output from multiple tools across…

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…

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AlmostSignifica…
Desktop

AlmostSignificant

An open-source platform for aggregating multiple sources of quality metrics as…

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…

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SAG-QC
Desktop

SAG-QC

Identifies and excludes non-target sequences independent of database. SAG-QC…

Identifies and excludes non-target sequences independent of database. SAG-QC calculates the probability that a sequence was derived from contaminants by comparing k-mer compositions with the no…

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QC-Chain
Desktop

QC-Chain

A fast, accurate and holistic NGS data quality-control method. The tool…

A fast, accurate and holistic NGS data quality-control method. The tool synergeticly comprised of user-friendly tools for (1) quality assessment and trimming of raw reads using Parallel-QC, a fast…

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HTQC
Desktop

HTQC High-Throughput Quality Control

A toolkit named for sequence reads quality control, which consists of six…

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…

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NGSQC
Desktop

NGSQC Next Generation Sequencing Quality Control

Provides a set of quality control measures to detect quality issues in deep…

Provides a set of quality control measures to detect quality issues in deep sequencing data derived from 2D surfaces. NGSQC is a comprehensive deep sequencing quality control pipeline that can help…

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QUASR
Desktop

QUASR Quality Assessment of Short Read

A lightweight pipeline written to process and analyse next-generation…

A lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms.

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SUGAR
Desktop

SUGAR SUbtile-based GUI-Assisted Refiner

Enables rapid evaluation and cleaning of the Illumina HiSeq and MiSeq data,…

Enables rapid evaluation and cleaning of the Illumina HiSeq and MiSeq data, specifically considering technical errors in flowcells and sequencing run.

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deepTools
Desktop
Web

deepTools

A Galaxy based web server for processing and visualizing deeply sequenced data.…

A Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable…

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NGS-Bits
Desktop

NGS-Bits

Permits quality control of Next-Generation-Sequencing (NGS) tumor-normal…

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…

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Index_investiga…
Desktop

Index_investigator

Tests if index switching is occurring in a given dataset. Index_investigator is…

Tests if index switching is occurring in a given dataset. Index_investigator is a script that provides a way to visualize switch for sequenced genomic datasets. This method shows that in samples,…

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Lacer
Desktop

Lacer

Recalibrates base quality scores without assuming knowledge of correct and…

Recalibrates base quality scores without assuming knowledge of correct and incorrect bases and without requiring knowledge of common variants. Lacer is an accurate base recalibrator. It enhances…

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Zseq
Desktop

Zseq

Identifies the most informative genomic sequences and reduces the number of…

Identifies the most informative genomic sequences and reduces the number of biased sequences, sequence duplications, and ambiguous nucleotides. Zseq is a linear method that finds the complexity of…

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QASDRA
Desktop

QASDRA Quality Assessment of Sequencing Data via Range Analysis

Detects ranges and introduces new metrics computed from their lengths. QASDRA…

Detects ranges and introduces new metrics computed from their lengths. QASDRA creates the quality assessment report of an input FASTQ file according to the user specified k and v parameters. The…

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RECKONER
Desktop

RECKONER Read Error Corrector Based on KMC

Corrects of genome sequencing reads, present especially in Illumina reads.…

Corrects of genome sequencing reads, present especially in Illumina reads. RECKONER is a read-error-correction algorithm, able to process eukaryotic close to 500 Mbp real sequencing data using less…

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Pyrocleaner
Desktop

Pyrocleaner

It is intended to clean the reads included in the sff file in order to ease the…

It is intended to clean the reads included in the sff file in order to ease the assembly process.

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poretools
Desktop

poretools

A flexible toolkit for exploring datasets generated by nanopore sequencing…

A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. Poretools operates directly on the native…

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BIGpre
Desktop

BIGpre

A quality assessment package for next-genomics sequencing data. BIGpre contains…

A quality assessment package for next-genomics sequencing data. BIGpre contains all the functions of other quality assessment software, such as the correlation between forward and reverse reads, read…

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MVA-NGS
Desktop

MVA-NGS Minority Variant Analyzer for NGS data

Detects and corrects artifactual minority variants. MVA-NGS increases data…

Detects and corrects artifactual minority variants. MVA-NGS increases data resolution and could aid both past and future studies incorporating high-throughput sequencing (HTS). It improves the…

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Rqc
Desktop

Rqc

Allows quality control and assessment of high-throughput sequencing data. Rqc…

Allows quality control and assessment of high-throughput sequencing data. Rqc performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics. It…

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savR
Desktop

savR

Parses Illumina Sequence Analysis Viewer (SAV) files, access data, and generate…

Parses Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots. SavR offers functions to generate a folder of images that approximates the format of the folder that was…

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FastQt
Desktop

FastQt

Provides a quality control tool for high throughput sequence data. FastQt is…

Provides a quality control tool for high throughput sequence data. FastQt is the clone of FastQC application ported from Java to C++/Qt5. FastQt aims to provide a simple way to do some quality…

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StatsDB
Desktop

StatsDB

An open-source software package for storage and analysis of next generation…

An open-source software package for storage and analysis of next generation sequencing run metrics. StatsDB has been designed for incorporation into a primary analysis pipeline, either at the…

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G-CNV
Desktop

G-CNV GPU-copy number variation

A graphics processing unit (GPU)-based tool for preparing data to detect copy…

A graphics processing unit (GPU)-based tool for preparing data to detect copy number variations (CNVs) with read-depth methods. G-CNV can be used to (i) filter low-quality sequences, (ii) mask…

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poreminion
Desktop

poreminion

Additional tools for analyzing Oxford Nanopore minION data. poreminion contains…

Additional tools for analyzing Oxford Nanopore minION data. poreminion contains some tools that have been made on top of Aaron R. Quinlan's and Nicholas J. Loman's poretools, and therefore…

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qrqc
Desktop

qrqc Quick Read Quality Control

Quickly scans reads and gathers statistics on base and quality frequencies,…

Quickly scans reads and gathers statistics on base and quality frequencies, read length, and frequent sequences.

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Picard
Desktop

Picard

A set of tools (in Java) for working with next generation sequencing data in…

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

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mubiomics
Desktop

mubiomics

A set of scripts (mostly python) for processing reads generated by the Roche…

A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms.

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IDCheck
Desktop

IDCheck

Allows assessment of concordance between genotype (from SNP arrays or DNA…

Allows assessment of concordance between genotype (from SNP arrays or DNA sequencing) and gene expression (RNA-seq) samples.

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subN
Desktop

subN

Masks substitutes low quality base calls with ‘N’s (undetermined bases) in…

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…

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FaQCs
Desktop

FaQCs FastQ Quality Control Software

A software package that can rapidly process large volumes of data, and which…

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…

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SeqAssist
Desktop

SeqAssist

Takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for…

Takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for sequence alignment, and aims to provide a quick overview and basic statistics of NGS data. SeqAssist is a useful and…

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NG6
Dataset

NG6

A user-friendly information system able to manage large sets of sequencing…

A user-friendly information system able to manage large sets of sequencing data. It includes, a workflow environment already containing pipelines adapted to different input formats, different…

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PathoQC
Desktop

PathoQC

Pre-processes next-generation sequencing (NGS) data. PathoQC is based on…

Pre-processes next-generation sequencing (NGS) data. PathoQC is based on several of the most used quality control software approaches and combines their benefits to offer a variety of quality control…

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QPLOT
Desktop

QPLOT

An automated tool that can facilitate the quality assessment of sequencing run…

An automated tool that can facilitate the quality assessment of sequencing run performance. Taking standard sequence alignments as input, QPLOT generates a series of diagnostic metrics summarizing…

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Dascrubber
Desktop

Dascrubber DAzzler Read SCRUBBing Suite

Provides a pipeline that one can use to scrub reads and if desired to scrub the…

Provides a pipeline that one can use to scrub reads and if desired to scrub the alignment piles. Dascrubber is a complete end-to-end scrubber for removing all artifacts and low quality segments from…

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basecallQC
Desktop

basecallQC

Provides package to work with Illumina bcl2Fastq software. basecallQC functions…

Provides package to work with Illumina bcl2Fastq software. basecallQC functions allow the user to update Illumina sample sheets, clean sample sheets of common problems such as invalid sample names…

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omnomicsQ
Desktop

omnomicsQ

Supports clinical labs with fast, simple and visual quality control of next…

Supports clinical labs with fast, simple and visual quality control of next generation sequencing bioinformatics data. omnomicsQ is developed to provide an objective, third party evaluation based on…

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stsPlots
Desktop

stsPlots

Plot primary analysis quality control metrics to assess potential SMRTcell…

Plot primary analysis quality control metrics to assess potential SMRTcell loading problems.

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Illuminate
Desktop

Illuminate

Python module and utilities to parse the metrics binaries output by Illumina…

Python module and utilities to parse the metrics binaries output by Illumina sequencers.

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NGS-TOOLBOX
Desktop

NGS-TOOLBOX

This collection of simple Perl scripts is adressed to scientists doing research…

This collection of simple Perl scripts is adressed to scientists doing research that bases on high throughput genomic/transcriptomic data.

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NxGview
Desktop

NxGview

A virtual software pipeline that contains several PERL modules for processing…

A virtual software pipeline that contains several PERL modules for processing next generation sequencing data.

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htseq-qa
Desktop

htseq-qa

Takes a file with sequencing reads (either raw or aligned reads) and produces a…

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.

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CorQ
Desktop

CorQ

Quality score based identification and correction of pyrosequencing errors.

Quality score based identification and correction of pyrosequencing errors.

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FastQ Screen
Desktop

FastQ Screen

Allows you to screen a library of sequences in FastQ format against a set of…

Allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

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FastQC
Desktop

FastQC

A quality control tool for high throughput sequence data. FastQC aims to…

A quality control tool for high throughput sequence data. FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.…

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FASTX-Toolkit
Desktop

FASTX-Toolkit

A collection of command line tools for Short-Reads FASTA/FASTQ files…

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…

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BAMStats
Desktop

BAMStats

A GUI desktop tool for calculating and displaying metrics to assess the success…

A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools.

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PIQA
Desktop

PIQA

A quality analysis pipeline designed to examine genomic reads produced by Next…

A quality analysis pipeline designed to examine genomic reads produced by Next Generation Sequencing technology (Illumina G1 Genome Analyzer). A short statistical summary, as well as tile-by-tile and…

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TileQC
Desktop

TileQC

Controls the quality of Solexa-based DNA sequence data. TileQC features both…

Controls the quality of Solexa-based DNA sequence data. TileQC features both qualitative and quantitative error detection. The guiding philosophy behind tileQC's qualitative error assessment…

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Hopper
Desktop

Hopper

Runs a series of programs that analyze data quality, assemble shotgun sequence…

Runs a series of programs that analyze data quality, assemble shotgun sequence data, and generates simple reports describing the results. The Hopper system was developed in order to prototype methods…

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