AlienTrimmer protocols

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AlienTrimmer specifications

Information


Unique identifier OMICS_01082
Name AlienTrimmer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for AlienTrimmer

AlienTrimmer in pipelines

 (4)
2018
PMCID: 5887026
PMID: 29622616
DOI: 10.1128/genomeA.00222-18

[…] 500 instrument using a 2 × 150-bp paired-end protocol, leading to 1,409,297 read pairs (>120× average sequencing depth, ∼250 bp insert size)., sequenced reads were clipped and trimmed with alientrimmer () and corrected with musket (). the remaining processed reads were assembled and scaffolded with spades (). the draft genome has a total size of 3,255,527 bp, represented in 204 […]

2017
PMCID: 5230755
PMID: 28081123
DOI: 10.1371/journal.pntd.0005216

[…] data were performed using the bcl2fastq software. trimming, clipping, and filtering off exogenous and/or non-confident bases (options:–q 13, -l 30, -p 80) within fastq files were performed with alientrimmer []. redundant or over-represented reads were reduced using the khmer software package (option:–c 70) []. finally, sequencing errors were corrected using musket [] and overlapping paired […]

2017
PMCID: 5607522
PMID: 28954001
DOI: 10.1590/0074-02760170019

[…] madison, wi, usa). after sequencing, all sequence reads were preprocessed to remove low-quality or artifactual bases. the fastqc 0.11.5 was used for assessing the quality of the raw data, and the alientrimmer 0.4.0 was used to trim and discard the reads with a phred quality score below 20. finally, the fqduplicate 1.1 was used to discard every duplicate paired-end read. the trimmed reads […]

2014
PMCID: 4271555
PMID: 25516620
DOI: 10.1128/mBio.02309-14

[…] were removed using the program sickle version 1.33 (github inc., san francisco, ca, usa). second, contaminant oligonucleotides (i.e., library adaptors) were detected and removed using the program alientrimmer (). third, reads that were below 45 nucleotides in length after performance of the cleaning steps described above were discarded, as were those containing more than 5% of the remaining […]

AlienTrimmer in publications

 (21)
PMCID: 5915733
PMID: 29691339
DOI: 10.1128/mBio.00573-18

[…] these tagged libraries resulted in ~12.6 million read pairs per strain on average. statistics of assembly for all the isolates are summarized in ., all sequenced reads were clipped and trimmed with alientrimmer v.0.4.0 (), corrected with musket v.1.1 (), merged (if needed) with flash v.1.2.11 (), and subjected to a digital normalization procedure with khmer v.2.0 (). for each sample, processed […]

PMCID: 5887026
PMID: 29622616
DOI: 10.1128/genomeA.00222-18

[…] 500 instrument using a 2 × 150-bp paired-end protocol, leading to 1,409,297 read pairs (>120× average sequencing depth, ∼250 bp insert size)., sequenced reads were clipped and trimmed with alientrimmer () and corrected with musket (). the remaining processed reads were assembled and scaffolded with spades (). the draft genome has a total size of 3,255,527 bp, represented in 204 […]

PMCID: 5864091
PMID: 29529083
DOI: 10.1371/journal.ppat.1006940

[…] rna sample prep kit illumina as per the manufacturers’ instructions. illumina hiseq2000 sequencer (multiplexing three samples per lane) was used to sequence libraries. sequences were cleaned with alientrimmer [] of adapter sequences. only high-quality sequences with a minimum of 30 nucleotides in length were considered for further analysis. cleaned genes were aligned to reference genomes […]

PMCID: 5721339
PMID: 29165566
DOI: 10.1093/gbe/evx236

[…] nextseq500 platform., all reads were preprocessed to remove low-quality or artifactual bases. library adapters at 5′ and 3′ ends and base pairs with a phred quality score <25 were trimmed using alientrimmer as implemented in galaxy (; ; ; ) (https://research.pasteur.fr/en/tool/pasteur-galaxy-platform/). reads with length <50 bp after these preprocessing steps or those containing >20% […]

PMCID: 5649026
PMID: 28827366
DOI: 10.1128/IAI.00541-17

[…] using a dneasy blood and tissue extraction kit (qiagen, denmark) and used for whole-genome sequencing on an illumina nextseq 500 (2 × 150 bp) platform (illumina, ca, usa). reads were trimmed with alientrimmer () to eliminate adapter sequences and discard reads with phred scores of ≤20. de novo assembly of illumina reads was performed using spades genome assembler, version 3.1 (). the complete […]

AlienTrimmer institution(s)
Institut Pasteur, Genotyping of Pathogens and Public Health Platform (PF8), Paris, France

AlienTrimmer review

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Desktop
simple, fast and useful tool