isONcorrect – Error Correction of ONT Transcriptomic Reads

isONcorrect

:: DESCRIPTION

isONcorrect is a tool for error-correcting Oxford Nanopore cDNA reads.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

isONcorrect

:: 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)

Hammer 0.2 – Error-correction of High-throughput Sequencing Datasets

Hammer 0.2

:: 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

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Hammer

:: 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.

Encore 1.31 – Polymorphism-friendly Error Correction

Encore 1.31

:: 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

  • Linux
  • Perl

:: DOWNLOAD

 Encore

:: 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.

TreeFix 1.1.10 / TreeFix-DTL 1.0.2 – Statistically Informed Gene Tree Error Correction using Species Trees

TreeFix 1.1.10 / TreeFix-DTL 1.0.2

:: 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

Yi-Chieh Wu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • C Compiler

:: DOWNLOAD

  TreeFix / TreeFix-DTL

:: 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.

BLESS v1p02 – Bloom-filter-based Error Correction Tool for NGS reads

BLESS v1p02

:: 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

BLESS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

  BLESS

:: 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.

ICC 2.0.1 – Insertion, Deletion and Carry-forward Error Correction for Next-generation Sequencing

ICC 2.0.1

:: 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

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 ICC

:: 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.

Lighter 1.1.2 – Fast and Memory-efficient Sequencing Error Correction without Counting

Lighter 1.1.2

:: 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

Li Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsx/Linux

:: DOWNLOAD

 Lighter

:: 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.

Pluribus / PluribusFast – Exploring the Limits of Error Correction Using a Suffix Tree

Pluribus / PluribusFast

:: DESCRIPTION

Pluribus utilizes a suffix tree to identify and correct sequencing errors in next generation sequencing data.

PluribusFast is a more efficient implementation of the Pluribus algorithm.

::DEVELOPER

Pluribus team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • JRE

:: DOWNLOAD

 Pluribus / PluribusFast

:: MORE INFORMATION

Citation

Pluribus – Exploring the Limits of Error Correction Using a Suffix Tree.
Savel D, LaFramboise T, Grama A, Koyuturk M.
IEEE/ACM Trans Comput Biol Bioinform. 2016 Jun 29.

Trowel 0.2.0.4 – Error Correction Module for Illumina Sequencing Reads

Trowel 0.2.0.4

:: DESCRIPTION

Trowel is an error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. This tool is the first tool that uses a quality threshold instead of a coverage cutoff in order to extract trusted k-mers.

::DEVELOPER

Trowel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

 Trowel

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 29. pii: btu513.
Trowel: a fast and accurate error correction module for Illumina sequencing reads.
Lim EC, Müller J, Hagmann J, Henz SR, Kim ST, Weigel D.

Coral 1.4.1 – Error Correction Algorithm for Correcting reads from DNA sequencing platforms

Coral 1.4.1

:: DESCRIPTION

Coral is 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. Coral can utilize also bases distant from the error in the correction process because the whole read is present in the alignment. Coral is easily adjustable to reads produced by different sequencing technologies like Illumina Genome Analyzer and Roche/454 Life Sciences sequencing platforms because the sequencing error model can be defined by the user.

::DEVELOPER

Jan Schröder , Leena Salmela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Coral

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Jun 1;27(11):1455-61. Epub 2011 Apr 5.
Correcting errors in short reads by multiple alignments.
Salmela L, Schröder J.