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Protocols

TraceTuner specifications

Information


Unique identifier OMICS_01158
Name TraceTuner
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Java, Perl
Computer skills Advanced
Version 3.0.6
Stability Beta
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens

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Versioning


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Documentation


TraceTuner citations

 (14)
library_books

High diversity of picornaviruses in rats from different continents revealed by deep sequencing

2016
PMCID: 5034103
PMID: 27530749
DOI: 10.1038/emi.2016.90

[…] (Life Technologies) with cycling conditions according to the manufacturer and with 40 cycles of amplification. Sanger sequencing was performed with the same amplification primers at Macrogen Europe. TraceTuner (v3.0.6beta) was used to format AB1 files from SANGER sequencing to fastq using -nocall -q options. Nucleotides with low-quality scores were trimmed using seqtk (https://github.com/lh3/seqt […]

library_books

Identification and characterization of Daldinia eschscholtzii isolated from skin scrapings, nails, and blood

2016
PeerJ
PMCID: 5178343
PMID: 28028453
DOI: 10.7717/peerj.2637

[…] 0 s, 58 °C for 30 s, and 72 °C for 60 s. The PCR products were then purified using Expin™ PCR SV (GeneAll, Korea), and confirmed by Sanger sequencing (First Base Laboratories Kuala Lumpur, Malaysia). TraceTuner version 3.0.6 () was used for base and quality calling of the sequenced ITS. The low-quality called bases (Phred value < 20) of both ends of the sequences were then trimmed by running Lucy […]

call_split

Identification of mammalian adapting mutations in the polymerase complex of an avian H5N1 influenza virus

2015
Nat Commun
PMCID: 4557292
PMID: 26082035
DOI: 10.1038/ncomms8491
call_split See protocol

[…] quimolar amounts of the individually barcoded libraries (which correspond to a single isolate). The pools were then sequenced on the Ion Torrent PGM with 314 chips. Basecalling was performed by using TraceTuner, and the resulting sequences were quality-trimmed and then assembled using the merger utility from the EMBOSS software suite. All processing steps were integrated into a reproducible Galaxy […]

call_split

Natural Yeast Promoter Variants Reveal Epistasis in the Generation of Transcriptional Mediated Noise and Its Potential Benefit in Stressful Conditions

2015
Genome Biol Evol
PMCID: 4419794
PMID: 25762217
DOI: 10.1093/gbe/evv047
call_split See protocol

[…] e 75 bp upstream of the start codon (supplementary table S7, Supplementary Material online). Sequencing was performed using an Applied Biosystems 3730xl DNA Analyzer. Base calling was performed using TraceTuner 3.0.4 beta () to obtain fasta and quality values. Vector and quality trimming were performed using Lucy 1.19p (). Only 96 reads were retained after trimming. Mapping reads was performed usi […]

library_books

Snow Surface Microbiome on the High Antarctic Plateau (DOME C)

2014
PLoS One
PMCID: 4125213
PMID: 25101779
DOI: 10.1371/journal.pone.0104505

[…] quality trimming approach was applied using a sliding window of 100 nt length with a cut-off on the Phred score of 30 and 20 for pyrosequencing and Sanger reads, respectively. For Sanger, we used the TraceTuner software (3.0.6; http://sourceforge.net/projects/tracetuner/) in order to convert the quality files in Phred score. All reads were aligned to the Silva reference database (http://www.mothur […]

library_books

A Five Year Survey of Dematiaceous Fungi in a Tropical Hospital Reveals Potential Opportunistic Species

2014
PLoS One
PMCID: 4123927
PMID: 25098697
DOI: 10.1371/journal.pone.0104352

[…] esed in 1% (w/v) agarose gel at 120 V for 30 min, purified and sent for Sanger sequencing (1st Base Laboratories Kuala Lumpur, Malaysia). Base and quality calling of sequenced ITS was performed using TraceTuner v3.0.6 . Lucy version 1.20 and the included zapping.awk script was then run to trim low quality bases (Phred value <20) called by TraceTuner from both ends of the sequences. Cleaned sequen […]

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