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Error correction software tools | Whole-genome sequencing data analysis

Characterizing the errors generated by common high-throughput sequencing platforms and telling true genetic variation from technical artefacts are two interdependent steps, essential to many analyses such as single nucleotide variant calling,…
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Standalone…
Desktop

Standalone hamming

A package for error-correcting DNA barcodes. Hamming allows one run of a…

A package for error-correcting DNA barcodes. Hamming allows one run of a massively parallel pyrosequencer to process up to 1544 samples simultaneously. The tagged barcoding strategy can be used to…

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PoreSeq
Desktop

PoreSeq

An open source program and Python library for de novo sequencing, consensus and…

An open source program and Python library for de novo sequencing, consensus and variant calling on data from Oxford Nanopore Technologies' MinION platform. Features include: de novo error…

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LQS
Desktop

LQS

Computes an improved consensus sequence for the assembly. LQS uses accurate…

Computes an improved consensus sequence for the assembly. LQS uses accurate short-read data and/or Pacific Biosciences circular consensus reads to correct error-prone long reads sufficiently for…

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PBcR
Desktop

PBcR PacBio Corrected Reads

An approach that utilizes short, high-identity sequences to correct the error…

An approach that utilizes short, high-identity sequences to correct the error inherent in long, single-molecule sequences. PBcR, implemented as part of the Celera Assembler, trims and corrects…

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SGA
Desktop

SGA String Graph Assembler

Assembles large genomes from high coverage short read data. SGA is designed as…

Assembles large genomes from high coverage short read data. SGA is designed as a modular set of programs, which are used to form an assembly pipeline. SGA implements a set of assembly algorithms…

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FALCON
Desktop

FALCON

Allows alignment of long reads for consensus and assembly. FALCON is a set of…

Allows alignment of long reads for consensus and assembly. FALCON is a set of tools based on a hierarchical genome assembly process. The software follows a "Hierarchical Genome Assembly…

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Nanocorrect
Desktop

Nanocorrect

Improves the accuracy of our nanopore reads to around 97% after two rounds of…

Improves the accuracy of our nanopore reads to around 97% after two rounds of correction. Nanocorrect is a prototype nanopore correction pipeline. This pipeline is inspired by pbdagcon which used…

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BLESS
Desktop
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Quake
Desktop

Quake

A package to correct substitution sequencing errors in experiments with deep…

A package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.

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Reptile
Desktop

Reptile

Allows users to correct errors in short-read data from next-generation…

Allows users to correct errors in short-read data from next-generation sequencing (NGS). Reptile is a scalable short-read error correction method broadly based on the k-mer spectrum approach, but…

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ShoRAH
Desktop

ShoRAH Short Reads Assembly into Haplotypes

A computational method for quantifying genetic diversity in a mixed sample and…

A computational method for quantifying genetic diversity in a mixed sample and for identifying the individual clones in the population, while accounting for sequencing errors. This approach provides…

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UMI-tools
Desktop

UMI-tools Unique Molecular Identifiers-tools

Demonstrates the value of properly accounting for errors in unique molecular…

Demonstrates the value of properly accounting for errors in unique molecular identifiers (UMIs). UMI-tools removes PCR duplicates and implements a number of different UMI deduplication schemes. It…

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ECHO
Desktop

ECHO

An error correction algorithm designed for short-reads from next-generation…

An error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina's Genome Analyzer II.

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LoRMA
Desktop

LoRMA

A method for correcting long and highly erroneous sequencing reads. LoRMA shows…

A method for correcting long and highly erroneous sequencing reads. LoRMA shows that efficient alignment free methods can be applied to highly erroneous long read data. The current approach needs…

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SGA-ICE
Desktop

SGA-ICE SGA-Iteratively Correcting Errors

Implements iterative error correction by using modules from String Graph…

Implements iterative error correction by using modules from String Graph Assembler (SGA). SGA-ICE is an iterative error correction pipeline that runs SGA in multiple rounds of k-mer-based correction…

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SEECER
Desktop

SEECER SEquencing Error CorrEction for Rna reads

A sequencing error correction algorithm for RNA-seq data sets. SEECER takes the…

A sequencing error correction algorithm for RNA-seq data sets. SEECER takes the raw read sequences produced by a next generation sequencing platform like machines from Illumina or Roche. It removes…

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SHREC
Desktop

SHREC

A bioinformatics tool for error correction of HTS read data. SHREC can identify…

A bioinformatics tool for error correction of HTS read data. SHREC can identify erroneous reads with sensitivity and specificity of over 99% and 96% for simulated data with error rates of up to 3% as…

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Coral
Desktop

Coral

An error correction algorithm for correcting reads from DNA sequencing…

An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer.

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HiTEC
Desktop

HiTEC High Throughput Error Correction

Allows accurate error correction in high-throughput sequencing data, such as…

Allows accurate error correction in high-throughput sequencing data, such as those generated by the Illumina Genome Analyzer. HiTEC algorithm uses a thorough statistical analysis of the suffix array…

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Canu
Desktop

Canu

Is specifically designed for noisy single-molecule sequences. Canu introduces…

Is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while…

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Musket
Desktop

Musket

An efficient multistage k-mer based corrector for Illumina short read data.

An efficient multistage k-mer based corrector for Illumina short read data.

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Hammer
Desktop

Hammer

A tool for error correction of short read datasets with non-uniform coverage,…

A tool for error correction of short read datasets with non-uniform coverage, such as single-cell data.

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QuorUM
Desktop

QuorUM Quality Optimized Reads from the University of Maryland

An error corrector for Illumina reads. QuorUM is designed around the novel idea…

An error corrector for Illumina reads. QuorUM is designed around the novel idea of minimizing the number of distinct erroneous k-mers in the output reads and preserving the most true k-mers. It is…

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TRAPLINE
Desktop

TRAPLINE Transparent Reproducible and Automated PipeLINE

Integrates the best performing data analysis, data evaluation and annotation…

Integrates the best performing data analysis, data evaluation and annotation methods in a Transparent, Reproducible and Automated PipeLINE for RNA sequencing data processing (suitable for Illumina,…

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Nanocorr
Desktop

Nanocorr

An open-source hybrid error correction algorithm. Nanocorr was specifically…

An open-source hybrid error correction algorithm. Nanocorr was specifically developed for Oxford Nanopore reads, because existing packages were incapable of assembling the long read lengths (5-50…

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CUDA-EC
Desktop

CUDA-EC

Allows users to correct sequencing errors in high-throughput short-read data.…

Allows users to correct sequencing errors in high-throughput short-read data. CUDA-EC is an algorithm based on the spectral alignment problem and uses a Bloom filter data structure to take advantage…

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SysCall
Desktop

SysCall

A logistic regression based classifier distinguishing heterozygous sites from…

A logistic regression based classifier distinguishing heterozygous sites from systematic errors. Given a list of candidate heterozygous genomic locations and a SAM file of sequenced reads SysCall…

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Trowel
Desktop

Trowel

A massively parallelized and highly efficient error correction module for…

A massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k-mer spectrum. With…

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RACER
Desktop

RACER Rapid and Accurate Correction of Errors in Reads

Corrects errors in next-generation sequencing (NGS) data. RACER is an…

Corrects errors in next-generation sequencing (NGS) data. RACER is an application that belongs to the class of k-mer counting programs. It uses 2-bit encoding of nucleotides and random replacement of…

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Pollux
Desktop

Pollux

Enables to correct errors introduced by Illumina, Ion Torrent, and Roche 454…

Enables to correct errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies. Pollux is receptive to low depth sequencing regions and can correct errors in the presence of…

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Jabba
Desktop

Jabba

A hybrid method to correct long third generation reads by mapping them on a…

A hybrid method to correct long third generation reads by mapping them on a corrected de Bruijn graph that was constructed from second generation data. Unique to Jabba is that this mapping is…

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Frame-Pro
Desktop

Frame-Pro

A profile homology search tool for PacBio reads. Frame-Pro is a tool using…

A profile homology search tool for PacBio reads. Frame-Pro is a tool using Hidden Markov Model (HMM) and directed acyclic graph to correct the errors in DNA sequencing reads. It can also provide…

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ntHash
Desktop

ntHash

A hashing algorithm tuned for processing DNA/RNA sequences. ntHash provides a…

A hashing algorithm tuned for processing DNA/RNA sequences. ntHash provides a fast way to compute multiple hash values for a given k-mer, without repeating the whole procedure for each value. To do…

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CoLoRMap
Desktop

CoLoRMap

Corrects noisy long reads, such as the ones produced by PacBio sequencing…

Corrects noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads. CoLoRMap is based on two novel ideas:…

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Lighter
Desktop

Lighter LIGHTweight ERror corrector

A fast and memory-efficient k-mer based error corrector. Unlike other error…

A fast and memory-efficient k-mer based error corrector. Unlike other error correctors using counting to obtain the solid kmers, Lighter has a novel sampling technique and uses only two bloom filters.

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Rcorrector
Desktop

Rcorrector

A k-mer based method to correct random sequencing errors in Illumina RNA-seq…

A k-mer based method to correct random sequencing errors in Illumina RNA-seq reads. Rcorrector uses a De Bruijn graph to compactly represent all trusted k-mers in the input reads. Unlike WGS read…

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Pacasus
Desktop

Pacasus

Corrects palindromic, long, error-rich reads without the loss of nucleotide…

Corrects palindromic, long, error-rich reads without the loss of nucleotide information. Pacasus aligns the read’s reverse complement to itself and splits the read in two smaller reads at the…

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ANAQUIN
Desktop

ANAQUIN

Facilitates the analysis of spike-in controls for next generation sequencing…

Facilitates the analysis of spike-in controls for next generation sequencing (NGS). ANAQUIN offers a way for users to evaluate the performance of spike-in controls and the accompanying RNA/DNA…

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LRCstats
Desktop

LRCstats

Provides a novel way to measure the accuracy of sequencing errors correction…

Provides a novel way to measure the accuracy of sequencing errors correction methods in case where realistic simulators exist. LRCstats has been developed to complement the SimLORD simulator for…

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HECIL
Desktop

HECIL Hybrid Error Correction with Iterative Learning

Allows decomposition of the workload into independent data-parallel tasks that…

Allows decomposition of the workload into independent data-parallel tasks that can be executed simultaneously. HECIL is a hybrid correction framework that computes erroneous long reads based on…

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MultiRes
Desktop

MultiRes

Uses a collection of sizes of k-mers as features for detecting sequencing…

Uses a collection of sizes of k-mers as features for detecting sequencing errors and rare variants. MultiRes is a reference-free k-mer based on error detection algorithm for a viral population. The…

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HALC
Desktop

HALC High Throughput Algorithm for Long Read Error Correction

Allows long read error correction. HALC aligns the long reads to short read…

Allows long read error correction. HALC aligns the long reads to short read contigs from the same species with a relatively low identity requirement so that a long-read region can be aligned to at…

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SQANTI
Desktop

SQANTI Structural and Quality Annotation of Novel Transcript Isoforms

Provides a wide range of descriptors of transcript quality and generates a…

Provides a wide range of descriptors of transcript quality and generates a graphical report to aid in the interpretation of the sequencing results. SQANTI is a pipeline for the in-depth…

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UMI-Reducer
Desktop

UMI-Reducer Unique Molecular Identifiers Reducer

Processes and differentiates polymerase chain reaction (PCR) duplicates from…

Processes and differentiates polymerase chain reaction (PCR) duplicates from biological duplicates. UMI-Reducer uses Unique Molecular Identifiers (UMIs) and the mapping position of the read to…

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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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iCORN
Desktop

iCORN Iterative Correction of Reference Nucleotides

Aligns deep coverage of short sequencing reads to correct errors in reference…

Aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. iCORN last version is based on SMALT (mapper), samtools, GATK, snp-o-matic…

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Karect
Desktop

Karect KAUST Assembly Read Error Correction Tool

An error correction technique based on multiple alignment. Karect supports…

An error correction technique based on multiple alignment. Karect supports substitution, insertion and deletion errors. It can handle non-uniform coverage as well as moderately covered areas of the…

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ACE
Desktop

ACE Accurate Correction of Errors

Corrects substitution errors in an Illumina archive using a k-mer trie. On real…

Corrects substitution errors in an Illumina archive using a k-mer trie. On real MiSeq and HiSeq Illumina archives, ACE yields higher gains in terms of coverage depth, outperforming state-of-the-art…

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BFC
Desktop

BFC

A free, fast and easy-to-use sequencing error corrector designed for Illumina…

A free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on greedy…

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GeneScissors
Desktop

GeneScissors

A comprehensive approach to detecting and correcting spurious transcriptome…

A comprehensive approach to detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment.

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EDAR
Algorithm

EDAR

Allows processing read data prior to sequence assembly. EDAR is an algorithm…

Allows processing read data prior to sequence assembly. EDAR is an algorithm that focuses on data generated from genomic shotgun sequencing techniques. This algorithm determines the most likely error…

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LSCplus
Desktop

LSCplus

Improves long reads accuracy by short read alignment. LSCplus overcomes the…

Improves long reads accuracy by short read alignment. LSCplus overcomes the disadvantage of LSC’s time consumption and improves quality. Only 1/3-1/4 of the time and 1/20-1/25 of the error…

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ADEPT
Desktop

ADEPT A Dynamic Error-detection Program with Trimming

Dynamically assesses errors within reads based on position-specific and local…

Dynamically assesses errors within reads based on position-specific and local quality scores. ADEPT is the first tool that we are aware of that dynamically processes data and relies on within-dataset…

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DecGPU
Desktop

DecGPU Distributed short read error correction on GPUs

Parallel and distributed error correction algorithm for high-throughput short…

Parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.

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NaS
Desktop

NaS Nanopore Synthetic-long

A hybrid approach developed to take advantage of data generated using MinION…

A hybrid approach developed to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore technologies to produce NaS reads of up to 60 kb that aligned with no…

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SleepEtAl2013
Algorithm

SleepEtAl2013

Corrects sequencing error in data from Illumina Solexa sequencing technology.…

Corrects sequencing error in data from Illumina Solexa sequencing technology. The algorithm is a method for modelling sequencing errors that can incorporate known sources of error intrinsic to the…

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MiRCA
Desktop

MiRCA MinIon Reads Correction Algorithm

Detects and corrects errors using preassembled Illumina short reads. MIRCA uses…

Detects and corrects errors using preassembled Illumina short reads. MIRCA uses an alignment-based approach, supports substitution, insertion and deletion errors, using pre-assembled short reads as a…

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MECAT
Desktop

MECAT Mapping Error Correction and de novo Assembly Tool

Employs novel alignment and error correction algorithms that are much more…

Employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and error correction tools. MECAT can be used for effectively de novo assembling…

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Pluribus
Desktop

Pluribus

An effective method for correcting sequencing errors using a generalized suffix…

An effective method for correcting sequencing errors using a generalized suffix trie. PLURIBUS utilizes multiple manifestations of an error in the trie to accurately identify errors and suggest…

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ABruijn…
Desktop

ABruijn assembler

Assembles long error-prone reads using de Bruijn graphs. While the running time…

Assembles long error-prone reads using de Bruijn graphs. While the running time of overlap-layout-consensus (OLC) assemblers is dominated by the overlap detection step, the running time of the…

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Fiona
Desktop

Fiona

An accurate parameter-free read error-correction method that can be run on…

An accurate parameter-free read error-correction method that can be run on inexpensive hardware and can make use of multicore parallelization whenever available.

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LoRDEC
Desktop

LoRDEC

A hybrid error correction method that builds a succinct de Bruijn graph…

A hybrid error correction method that builds a succinct de Bruijn graph representing the short reads, and seeks a corrective sequence for each erroneous region in the long reads by traversing chosen…

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proovread
Desktop

proovread

A hybrid correction pipeline for SMRT reads, which can be flexibly adapted on…

A hybrid correction pipeline for SMRT reads, which can be flexibly adapted on existing hardware and infrastructure from a laptop to a high-performance computing cluster.

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Blue
Desktop

Blue

Corrects sequencing errors. Blue is a k-spectrum algorithm that uses read…

Corrects sequencing errors. Blue is a k-spectrum algorithm that uses read context to choose between alternative replacement k-mers, with the overall goal of minimizing the number of changes needed to…

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EC
Desktop

EC Error Corrector

An efficient, scalable, and robust error correction algorithm for correcting…

An efficient, scalable, and robust error correction algorithm for correcting short reads. The steps of EC can be broken into three independent tasks. At first it builds k-mers and hashes the k-mers…

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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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sprai
Desktop

sprai single pass read accuracy improver

Corrects sequencing errors in single-pass reads for de novo assembly. Sprai is…

Corrects sequencing errors in single-pass reads for de novo assembly. Sprai is an application designed to correct sequencing errors in single-molecule DNA sequencing reads, especially in Continuous…

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CloudRS
Desktop

CloudRS

Corrects sequencing errors in next-generation sequencing (NGS) data. CloudRS is…

Corrects sequencing errors in next-generation sequencing (NGS) data. CloudRS is a MapReduce application, based on the multiple sequence alignment (MSA) approache, that emulates the concept of the…

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GuEtAl2015
Desktop

GuEtAl2015

Allows to treat sequencing errors. This method consists in a disk-based…

Allows to treat sequencing errors. This method consists in a disk-based sequencing error correction method. The concept is based on a special on-disk index structure named the BoND-tree. This…

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PAGANtec
Algorithm

PAGANtec PAGAN transcriptome error correction

Allows users to treat error correction about next-generation sequencing data.…

Allows users to treat error correction about next-generation sequencing data. PAGANtec is based on the PAGAN graph structure and it is parallelized with OpenMP.

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Scrible
Algorithm

Scrible

Represents a clone-by-clone protocol that treats combinatorial pooling design…

Represents a clone-by-clone protocol that treats combinatorial pooling design to overcome the limitations of DNA barcoding. Scrible tries to take care of the problem of correcting the short reads…

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RNASeqBias
Desktop

RNASeqBias

Detects and corrects biases in RNA-Sequencing data. RNASeqBias is an R package…

Detects and corrects biases in RNA-Sequencing data. RNASeqBias is an R package that contains functions and sample data to check correlation between gene expression measures obtained from different…

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CallSim
Desktop

CallSim

A software application that provides evidence for the validity of base calls…

A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data.

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EULER-AIR
Desktop

EULER-AIR

Detects and corrects base assignment errors in genome assembly projects.…

Detects and corrects base assignment errors in genome assembly projects. EULER-AIR is based on an Expectation-Maximization (EM) algorithm and can help to design efficient finishing experiments…

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Hybrid SHREC
Desktop

Hybrid SHREC

Represents an error correction tool that permits to correct insertions,…

Represents an error correction tool that permits to correct insertions, deletions and substitutions in a mixed set of reads produced by various sequencing platforms. HSHREC is made for the hybrid…

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LSC
Desktop

LSC

A method for the combined analysis of data from second generation sequencers…

A method for the combined analysis of data from second generation sequencers and third generation sequencers, with the former delivering a massive (108) number of accurate short reads and the latter…

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HErCoOl
Desktop

HErCoOl High-throughput Error Correction by Oligomers

Represents an error correction algorithm based on k-mer strings. HErCoOl…

Represents an error correction algorithm based on k-mer strings. HErCoOl supplies an error correction method of next generation sequencing (NGS) data, and more particularly for mixed samples. This…

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Redeem
Desktop

Redeem Read Error DEtection and Correction via Expectation Maximization

Identifies and corrects read errors, targeting at repetitive genomes. Redeem is…

Identifies and corrects read errors, targeting at repetitive genomes. Redeem is different from existing methods for identifying sequencing errors. It models genome repetition and can be fed with…

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SleepEC
Desktop

SleepEC

A method for the correction of sequencing errors in data from the Illumina…

A method for the correction of sequencing errors in data from the Illumina Solexa sequencing platforms. SleepEC does not require a reference genome and is of relevance for microRNA studies,…

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PREMIER
Algorithm

PREMIER

Corrects errors in high throughput DNA sequencing data. PREMIER’s approach…

Corrects errors in high throughput DNA sequencing data. PREMIER’s approach consists in a hidden Markov model for the DNA sequencer outputs.

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MyHybrid
Algorithm

MyHybrid

Represents a hybrid approach which is based on an alignment-free method…

Represents a hybrid approach which is based on an alignment-free method combined with multiple alignments. MyHybrid is able to construct suffix arrays on all short reads to search the correct…

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PSAEC
Algorithm

PSAEC

Represents an algorithm for short read error correction. PSAEC uses partial…

Represents an algorithm for short read error correction. PSAEC uses partial suffix arrays in high-throughput sequencing data. PSAEC can optimize the HiTEC program by using the h-order partial suffix…

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Qamar
Desktop

Qamar

Allows users to correct sequencing errors. Qamar is able to deal with long…

Allows users to correct sequencing errors. Qamar is able to deal with long reads of different lengths. It is also adapted to manage short reads. The implementation of this tool permits to handle…

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RECOUNT
Desktop

RECOUNT

Aims to reduce next generation sequencing (NGS) error rate. RECOUNT is an…

Aims to reduce next generation sequencing (NGS) error rate. RECOUNT is an implementation of an Expectation Maximization algorithm for tag count correction. Using both the reference genome and…

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BLISS
Desktop

BLISS Batch anaLysIS Suite

Helps identify batch effects in RNA expression data. BLISS has been tested on…

Helps identify batch effects in RNA expression data. BLISS has been tested on miRNA and mRNA results derived from the illumina sequencing platform.

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SOAPec
Desktop

SOAPec

The read correction package is a short-read correction tool and part of…

The read correction package is a short-read correction tool and part of SOAPdenovo . It is specially designed to correct Illumina GA short reads.

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Bloocoo
Desktop

Bloocoo

A k-mer spectrum-based read error corrector, designed to correct large datasets…

A k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint.

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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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PacBioToCA
Desktop

PacBioToCA

A module in the Celera Assembler software package that performs error…

A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads.

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Simplifier
Desktop

Simplifier

Enables to remove redundant Prokaryote sequences produced by genome assembly.…

Enables to remove redundant Prokaryote sequences produced by genome assembly. Simplifier is a stand-alone application that was developed to (i) eliminate redundant sequences from groups of contigs…

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