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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 citations

 (10)
call_split

Transcriptome sequencing and delimitation of sympatric Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA

2017
PLoS One
PMCID: 5593202
PMID: 28892487
DOI: 10.1371/journal.pone.0183002
call_split See protocol

[…] edundant transcripts, and removal of noise transcripts) was performed according to the protocol described in Peña and colleagues []. Within the error correction step, parameter values supplied to the Reptile error correction software v1.1 [] for the O. pearsei sp. nov. read set were as follows (see methods in [] for a description of how these values were derived): T_expGoodCnt of 54, T_card of 21, […]

library_books

High Throughput Sequencing Based Immune Repertoire Study during Infectious Disease

2016
Front Immunol
PMCID: 5005336
PMID: 27630639
DOI: 10.3389/fimmu.2016.00336

[…] luding 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. […]

library_books

A comparative study of k spectrum based error correction methods for next generation sequencing data analysis

2016
Hum Genomics
PMCID: 4965716
PMID: 27461106
DOI: 10.1186/s40246-016-0068-0

[…] lemented in four of the six investigated methods to allow compression of the filter, storage of count data, and representation of maps in addition to sets [] (also see Table ). The other two methods (Reptile and Trowel) used hash tables, which do not yield false positive. Although Bloom filter’s space efficiency comes at the cost of false positives, all major error correction programs have reduced […]

library_books

Global priorities for national carnivore conservation under land use change

2016
Sci Rep
PMCID: 4817124
PMID: 27034197
DOI: 10.1038/srep23814

[…] common birds, amphibians, mammals and reptiles (). Under expected land use change (), at the 17% target for terrestrial land protection, carnivore surrogacy for threatened bird, amphibian, mammal and reptile species also decreased, with the largest drop in representation occurring for endangered (10% decrease) and critically endangered (~14% decrease) bird, amphibian, mammal and reptile species () […]

library_books

In search of perfect reads

2015
BMC Bioinformatics
PMCID: 4674851
PMID: 26679555
DOI: 10.1186/1471-2105-16-S17-S7

[…] The authors thank Sriram P. Chockalingam for his support in understanding the implementation of Reptile. This work is supported in part by the National Science Foundation under ATD-1120597, CCF-1360593 and IIS-1416259, and a Department of Science and Technology Swarnajayanti Fellowship from the […]

library_books

De Novo Assembly and Characterization of the Invasive Northern Pacific Seastar Transcriptome

2015
PLoS One
PMCID: 4631335
PMID: 26529321
DOI: 10.1371/journal.pone.0142003

[…] ly-confounding 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, as some […]

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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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