:: DESCRIPTION
isONcorrect is a tool for error-correcting Oxford Nanopore cDNA reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Kristoffer Sahlin, Botond Sipos, Phillip L James, Daniel Turner, Paul Medvedev,
Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis
(bioRxiv, 2020)
:: DESCRIPTION
Hammer is a tool for error correction of short read datasets with non-uniform coverage, such as single-cell data. In particular, Hammer does not make any uniformity assumptions on the distribution of the reads along the genome. It is based on a combination of the Hamming graph build from the set of k-mers and a simple probabilistic model for sequencing errors
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Medvedev, P., Scott, E., Kakaradov, B., Pevzner, P.,
Error correction of high-throughput sequencing datasets with non-uniform coverage,
Bioinformatics (2011) 27 (13): i137-i141.
:: DESCRIPTION
Encore is a sequencing error correction tool that is designed for highly polymorphic genome sequencing projects. It can be used as a preprocessing tool for de novo assembly or as a read correction tool for any other purpose. It supports multiple NGS platforms and is suitable for low-polymorphism datasets as well as datasets with high SNP and micro-indel rates.
::DEVELOPER
Nilgun Donmez and Michael Brudno
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nilgun Donmez and Michael Brudno (2011)
Hapsembler: an assembler for highly polymorphic genomes.
In Proceedings of the 15th Annual international conference on Research in computational molecular biology (RECOMB’11), Springer-Verlag, Berlin, Heidelberg, 38-52.
:: DESCRIPTION
TreeFix is a phylogenetic method for improving gene tree reconstructions using a test statistic for likelihood equivalence and a species tree aware (reconciliation) cost function.
TreeFix-DTL is a phylogenetic program for reconstructing highly accurate prokaryotic gene trees.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees
Yi-Chieh Wu, Matthew D. Rasmussen, Mukul S. Bansal, and Manolis Kellis.
Systematic Biology. 2013. doi: 10.1093/sysbio/sys076
Improved Gene Tree Error-Correction in the Presence of Horizontal Gene Transfer.
Bansal MS, Wu YC, Alm EJ, Kellis M.
Bioinformatics. 2014 Dec 5. pii: btu806.
:: DESCRIPTION
BLESS (BLoom-filter-based Error correction Solution for high-throughput Sequencing reads) is a novel algorithm that produces accurate correction results with much less memory compared with previous solutions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 May 15;30(10):1354-62. doi: 10.1093/bioinformatics/btu030. Epub 2014 Jan 21.
BLESS: bloom filter-based error correction solution for high-throughput sequencing reads.
Heo Y1, Wu XL, Chen D, Ma J, Hwu WM.
:: DESCRIPTION
ICC (Indel and Carryforward Correction) is a software pipeline to analyze 454 pyrosequencing data, including read quality filtering and alignment, indel and carryforward error correction, single nucleotide variant calling, and calculation of nucleotide variant and hyplotype frequencies.
::DEVELOPER
Mullins Molecular Retrovirology Lab, University of Washington.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Oct 1;29(19):2402-9. doi: 10.1093/bioinformatics/btt434. Epub 2013 Jul 29.
Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.
Deng W1, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI.
:: DESCRIPTION
Lighter is a kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2014;15(11):509.
Lighter: fast and memory-efficient sequencing error correction without counting.
Song L, Florea L, Langmead B.
:: DESCRIPTION
EC is a novel error correction algorithm and compared it with four other state-of-the-art algorithms using both real and simulated sequencing reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
EC: an efficient error correction algorithm for short reads.
Saha S, Rajasekaran S.
BMC Bioinformatics. 2015;16 Suppl 17:S2. doi: 10.1186/1471-2105-16-S17-S2.
:: DESCRIPTION
KEC is a software for error threshold finding based on fitting of Poisson distribution to k-counts distribution was added.
::DEVELOPER
Georgia State University NGS Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
P. Skums, Z. Dimitrova, D. S. Campo, G. Vaughan, L. Rossi, J. C. Forbi, J. Yokosawa, A. Zelikovsky, Y. Khudyakov,
“Efficient error correction for next-generation sequencing of viral amplicons,”
BMC Bioinformatics 13 (Suppl10): S6 2012
:: DESCRIPTION
CUDA-EC is a scalable parallel algorithm for correcting sequencing errors in high-throughput short-read data so that error-free reads can be available before DNA fragment assembly.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Comput Biol. 2010 Apr;17(4):603-15. doi: 10.1089/cmb.2009.0062.
A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware.
Shi H, Schmidt B, Liu W, Müller-Wittig W.
