Reptile protocols

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Reptile specifications

Information


Unique identifier OMICS_01109
Name Reptile
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1
Stability No
Requirements
Perl, GNU make, C++ compiler
Maintained No

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Additional information


A parallelized version is available at http://aluru-sun.ece.iastate.edu/lib/exe/fetch.php?media=source:reptile-omp.tar.bz2 Tutorial: http://aluru-sun.ece.iastate.edu/doku.php?id=reptile_tutorial

Publications for Reptile

Reptile in pipelines

 (2)
2017
PMCID: 5593202
PMID: 28892487
DOI: 10.1371/journal.pone.0183002

[…] pearsei sp. nov., with the addition of the directive tophred33, as the reads were produced by an earlier generation sequencing machine. during the error correction step, parameter values supplied to reptile were as follows: t_expgoodcnt of 10, t_card of 4, kmerlen of 13, qthreshold of 66, qlb of 58, maxbadqperkmer of 8 and step to 12, with all other settings at their defaults. for initial de […]

2015
PMCID: 4719071
PMID: 26026159
DOI: 10.1093/bib/bbv029

[…] intensive tasks like de novo assembly. as a result, most tools only correct substitution errors (), and some even make the hamming distance their central concept: the k-mer frequency tools reptile [], hammer [] and bayeshammer [] create a hamming graph in which k-mers as nodes are connected by edges, if the hamming distance between them is below a certain very low threshold (d). […]


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Reptile in publications

 (8)
PMCID: 5005336
PMID: 27630639
DOI: 10.3389/fimmu.2016.00336

[…] k-mer spectrum, multiple sequence alignment, and suffix tree (). based on these algorithms, bioinformatic tools are designed for different platforms, for example, bfc (), hitec (), lighter (), reptile (), and echo () are for illumina platforms, and pyronoise (), denoiser (), and hector () are for 454 platforms. their main approaches, correction functions, and qualities are compared in ref. […]

PMCID: 4965716
PMID: 27461106
DOI: 10.1186/s40246-016-0068-0

[…] limitations of some newest k-spectrum-based methods and to provide recommendations for users in selecting suitable methods with respect to specific ngs datasets., six k-spectrum-based methods, i.e., reptile, musket, bless, bloocoo, lighter, and trowel, were compared using six simulated sets of paired-end illumina sequencing data. these ngs datasets varied in coverage depth (10× to 120×), read […]

PMCID: 4942974
PMID: 27413529
DOI: 10.1186/s13227-016-0050-x

[…] qthreshold to 73, maxbadqperkmer to 8, and kmerlen to 25 (to match the k-mer length used in trinity). (3) rerunning “seq-analy” using the adjusted input settings. (4) creating the input settings to reptile based on the output of step 3. in our case, we set t_expgoodcnt to 44, t_card to 17, kmerlen to 13, qthreshold to 73, qlb to 60, maxbadqperkmer to 8 and step to 12, leaving all other settings […]

PMCID: 4674851
PMID: 26679555
DOI: 10.1186/1471-2105-16-S17-S7

[…] of the graph is to better estimate the validity of a kmer by taking its graph neighborhood into account. we use the same space efficient data structure to construct and store the hamming graph as in reptile (for details, see [])., our algorithm for processing a read is presented in algorithm 1. the algorithm decomposes a read into overlapping kmers such that the overlap between two consecutive […]

PMCID: 4631335
PMID: 26529321
DOI: 10.1371/journal.pone.0142003

[…] errors, certain specific sequence motifs can produce false positive base calling errors in illumina hiseq 2000 data [,]. to remove these systematic sequence read errors we utilized the reptile v1.1 error correction pipeline (http://aluru-sun.ece.iastate.edu/doku.php?id=reptile) []. an initial optimization run was conducted to determine the configuration for error correction, […]


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Reptile institution(s)
Computational Science Center IBM T. J. Watson Research, Cambridge, MA, USA; Georgia Institute of Technology, Atlanta, GA, USA; Georgia Institute of Technology, Atlanta, GA, USA

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