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AlienTrimmer specifications


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


No version available

Publication for AlienTrimmer

AlienTrimmer citations


Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole Genome Sequencing

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

[…] rom 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 r […]


Draft Genome Sequence of the Fish Pathogen Flavobacterium columnare Genomovar III Strain PH 97028 (=CIP 109753)

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

[…] on a NextSeq 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 scaffold […]


Pleiotropic roles of Clostridium difficile sin locus

PLoS Pathog
PMCID: 5864091
PMID: 29529083
DOI: 10.1371/journal.ppat.1006940
call_split See protocol

[…] tal 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 (FN54 […]


Double Face Meets the Bacterial World: The Opportunistic Pathogen Stenotrophomonas maltophilia

Front Microbiol
PMCID: 5684188
PMID: 29170656
DOI: 10.3389/fmicb.2017.02190

[…] uality score of the sequences of all strains was checked using FastQC v.0.11.2, to identify adapters and contaminant sequences remaining after sequencing. Contaminant sequences were removed using the AlienTrimmer v.0.4.0 software () and a customized database of adapters adding the contaminant sequences recognized by FastQC. Sequence trimming and filtering were performed by PRINSEQ-Lite () to filte […]


Spontaneous Loss of Virulence in Natural Populations of Listeria monocytogenes

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

[…] ted 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 […]


Polygala tenuifolia extract inhibits lipid accumulation in 3T3 L1 adipocytes and high fat diet–induced obese mouse model and affects hepatic transcriptome and gut microbiota profiles

PMCID: 5642193
PMID: 29056891
DOI: 10.1080/16546628.2017.1379861

[…] use written script; paired-end reads were joined using the PEAR program (Exelixis Lab, Heidelberg Institute for Theoretical Studies, German); primer sequences were trimmed from joined reads using the AlienTrimmer program; low-quality end sequences were trimmed off using sliding windows (five nucleotides) with an average quality value <10, and short sequences of <200 nucleotides were screened out u […]


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

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simple, fast and useful tool