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, haplotype inference, sequence…
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SGA
Desktop

SGA String Graph Assembler

A de novo genome assembler based on the concept of string graphs. The major…

A de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.…

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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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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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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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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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RACER
Desktop
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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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SHREC
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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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HiTEC
Desktop

HiTEC

Accurate error correction in high-throughput sequencing data.

Accurate error correction in high-throughput sequencing data.

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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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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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Reptile
Desktop

Reptile

A software tool developed in C++ for correcting sequencing errors in short…

A software tool developed in C++ for correcting sequencing errors in short reads from next-generation sequencing platforms. Reptile works with the spectrum of k-mers from the input reads, and…

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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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CUDA-EC
Desktop

CUDA-EC

An algorithm for correcting sequencing errors in high-throughput short-read…

An algorithm for correcting sequencing errors in high-throughput short-read data so that error-free reads can be available before DNA fragment assembly, which is of high importance to many…

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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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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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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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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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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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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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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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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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MiRCA
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Blue
Desktop

Blue

An error-correction algorithm based on k-mer consensus and context.

An error-correction algorithm based on k-mer consensus and context.

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Hybrid SHREC
Desktop

Hybrid SHREC

An error correction algorithm for correcting reads from various DNA sequencing…

An error correction algorithm for correcting reads from various DNA sequencing platforms.

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BLESS
Desktop
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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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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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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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