TriageTools protocols

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TriageTools specifications


Unique identifier OMICS_04587
Name TriageTools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format FASTQ
Operating system Unix/Linux
Programming languages Java
License Apache License version 2.0
Computer skills Advanced
Version 0.2.2
Stability Stable
Maintained Yes



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  • person_outline Vincent Detours <>

Additional information

Publication for TriageTools

TriageTools in pipeline

PMCID: 5164930
PMID: 27820796
DOI: 10.1038/nchembio.2226

[…] v3 chemistry. raw sequencing data is available from ena under accession number erp014134., reads were trimmed of adapter sequences using cutadapt (v.1.2.1). high-quality reads were extracted using triagetools (v0.2.2, long reads –length 35, high-quality bases –quality 9, and complex sequences –lzw 0.33). alignments onto the mm10 genome were carried out using gsnap (v2014-02-28) with gencode […]

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TriageTools in publications

PMCID: 5119491
PMID: 27482057
DOI: 10.15252/msb.20166890

[…] western lightning plus‐ecl (perkinelmer)., unaligned reads in fastq format were trimmed of adapter sequence agatcggaagagcacacgtctgaactccagtcac using cutadapt (v.1.2.1) and then partitioned using triagetools (fimereli et al, ) (v0.2.2) to select long (–length 35), high‐quality (–quality 9), and sequence‐complex (–lzw 0.33) reads. selected reads were aligned using gsnap (wu & nacu, ; […]

PMCID: 4374178
PMID: 25884932
DOI: 10.1186/s12885-015-1176-2

[…] and an e-value of e-05) against the refseq viral database. contigs with a viral hit were further aligned against the nt database and analyzed as in the two previous steps., in pipeline 4 we used triagetools [] (v0.2.0), a tool that efficiently screens input reads for similarity to a specific target sequence. triagetools was utilized with default parameters, the raw reads as input […]

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TriageTools institution(s)
IRIBHM, Universite Libre de Bruxelles, Brussels, Belgium; Welbio, Universite Libre de Bruxelles, Brussels, Belgium
TriageTools funding source(s)
Supported by TeleVie grant from the Belgian FNRS.

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