SHREC : (Short Read Error Correction) A bioinformatics tool for error correction of HTS read data.
TagDust : A Program to eliminate artifactual reads from next-generation sequencing data sets.
AYB : A base caller for the Illumina Genome Analyzer, using an explicit statistical model of how errors occur during sequencing to produce more accurate reads from the raw intensity data.
BayesCall : A model-based basecalling algorithm for high-throughput short-read sequencing
Ibis : (Improved base identification system), is an accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads.
Swift : Open source primary data analysis for next-gen DNA sequencers.
QuorUM : (Quality Optimized Reads from the University of Maryland) An error corrector for Illumina reads.
HiTEC : Accurate error correction in high-throughput sequencing data.
Musket : (multistage k-mer spectrum based corrector) An efficient multistage k-mer based corrector for Illumina short read data.
ECHO : An error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina's Genome Analyzer II.
Trowel : An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach.
Reptile : A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms.
HECTOR : A parallel multistage k-hopo spectrum based homopolymer-length error corrector for 454 sequencing data.
DecGPU : (DecGPU - Distributed error correction on CPU/GPU clusters) Parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.
Hybrid SHREC : An error correction algorithm for correcting reads from various DNA sequencing platforms.
HTQC : A toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.
QC-Chain : 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.
NGS QC Toolkit : A toolkit for the quality control (QC) of next generation sequencing (NGS) data.
Kraken : A set of tools for quality control and analysis of high-throughput sequence data.