SLIP 1.0.1 / SLIDE 1.0.4 – Rapid Multiple Hypothesis Testing Correction / Power Estimation

SLIP 1.0.1 / SLIDE 1.0.4

:: DESCRIPTION

SLIP (Sliding-window method for Locally Inter-correlated markers for Power estimation) is a multivariate normal distribution (MVN)-based power estimation method. SLIP shows a near identical accuracy to the standard simulation procedure for power, and is much faster.

::DEVELOPER

ZarLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX

:: DOWNLOAD

SLIP / SLIDE

:: MORE INFORMATION

Citation

Buhm Han, Hyun Min Kang, and Eleazar Eskin (2009)
Rapid and accurate multiple testing correction and power estimation for millions of correlated markers.
PLoS Genet 5(4): e1000456. doi:10.1371/journal.pgen.1000456

LRCstats – Evaluating Long Reads Correction tools

LRCstats

:: DESCRIPTION

LRCstats is an open-source pipeline for benchmarking DNA long read correction algorithms for long reads outputted by third generation sequencing technology such as machines produced by Pacific Biosciences.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

LRCstats

:: MORE INFORMATION

Citation

La S, Haghshenas E, Chauve C.
LRCstats, a tool for evaluating long reads correction methods.
Bioinformatics. 2017 Nov 15;33(22):3652-3654. doi: 10.1093/bioinformatics/btx489. PMID: 29036421.

Chimericognizer – Optical Map based Chimeric Contigs Correction tool

Chimericognizer

:: DESCRIPTION

Chimericognizer is a novel and accurate chimeric contigs correction tool which can correct chimeric contigs and chimeric optical map molecules by each other.

::DEVELOPER

Weihua Pan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

Chimericognizer

:: MORE INFORMATION

Citation

Pan W, Lonardi S.
Accurate detection of chimeric contigs via Bionano optical maps.
Bioinformatics. 2019 May 15;35(10):1760-1762. doi: 10.1093/bioinformatics/bty850. PMID: 30295726.

Pipasic 20140121 – Protein Abundance Correction in Metaproteomic Data

Pipasic 20140121

:: DESCRIPTION

Pipasic (peptide intensity-weighted proteome abundance similarity correction) is a tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework.

::DEVELOPER

Bernhard Y. Renard

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ WIndows/ MacOsX
Python
BioPython

:: DOWNLOAD

Pipasic

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):i149-i156. doi: 10.1093/bioinformatics/btu267.
Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics.
Penzlin A, Lindner MS, Doellinger J, Dabrowski PW, Nitsche A, Renard BY

PolytomySolverNAD 0.1 – Polytomy Refinement for the Correction of Dubious Duplications in Gene Trees

PolytomySolverNAD 0.1

:: DESCRIPTION

Given a rooted binary gene tree and species tree, PolytomySolverNAD corrects a NAD (Non-Apparent Duplication) of the gene tree by applying multifurcation.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

PolytomySolverNAD

:: MORE INFORMATION

Citation

Polytomy refinement for the correction of dubious duplications in gene trees.
Lafond M, Chauve C, Dondi R, El-Mabrouk N.
Bioinformatics. 2014 Sep 1;30(17):i519-i526. doi: 10.1093/bioinformatics/btu463.

ParalogyCorrector – Gene Tree Correction

ParalogyCorrector

:: DESCRIPTION

Given a gene tree, a species tree and a list of gene pairs that are required to be orthologs, ParalogyCorrector finds a gene tree as close as possible to the original that satisfies these constraints under reconciliation.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

ParalogyCorrector

:: MORE INFORMATION

Citation

Lafond M, Semeria M, Swenson K M, Tannier E, El-Mabrouk N :
Gene tree correction guided by orthology
BMC Bioinformatics 14:S5I; 10.1186/1471-2105-14-S15-S5-T, 2013.

TAEC – an R package for Taxonomic Analysis by Elimination and Correction

TAEC

:: DESCRIPTION

TAEC, a new homology-based approach for taxonomic analysis, utilizes the similarity in the genomic sequence in addition to the result of an alignment tool.

::DEVELOPER

Lingling An

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

TAEC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jul 16;15:242. doi: 10.1186/1471-2105-15-242.
Accurate genome relative abundance estimation for closely related species in a metagenomic sample.
Sohn MB, An L1, Pookhao N, Li Q.

AutoEditor 1.20 – Automated Correction of Genome Sequence Errors

AutoEditor 1.20

:: DESCRIPTION

AutoEditor is a tool for correcting sequencing and basecaller errors using sequence assembly and chromatogram data. On average AutoEditor corrects 80% of erroneous base calls, with an accuracy of 99.99%.This in turn improves the overall accuracy of genome sequences and facilitates the use of these sequences for polymorphism discovery.

::DEVELOPER

the Center for Bioinformatics and Computational Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

AutoEditor

:: MORE INFORMATION

Citation

“Automated correction of genome sequence errors.”
Gajer P, Schatz M, Salzberg SL,
Nucleic Acids Research, 2004. 32(2):562-9.

Reptile 1.1 – Short Read Error Correction

Reptile 1.1

:: DESCRIPTION

Reptile (Representative tiling) corrects sequencing errors in short reads (32bp ~ 150bp) generated by next-gen sequencing platforms, e.g. Illumina.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler
Perl

:: DOWNLOAD

Reptile

:: MORE INFORMATION

Citation

X. Yang, K. Dorman and S. Aluru,
“Reptile: Representative tiling for short read error correction”,
Bioinformatics, 26(20), 2526-2533, 2010.

proovread 2.14.1 – Large-scale high accuracy PacBio Correction through iterative Short Read Consensus.

proovread 2.14.1

:: DESCRIPTION

proovread is 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.

::DEVELOPER

Department of Bioinformatics, University of Würzburg,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
SHRiMP2
bash version 4 or above

:: DOWNLOAD

proovread

:: MORE INFORMATION

Citation:

proovread: large-scale high accuracy PacBio correction through iterative short read consensus.
Hackl T, Hedrich R, Schultz J, Förster F.
Bioinformatics. 2014 Jul 10. pii: btu392.