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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 citations

 (22)
library_books

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

2018
MBio
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 […]

library_books

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

2018
Genome Announc
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 […]

library_books

Pleiotropic roles of Clostridium difficile sin locus

2018
PLoS Pathog
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 […]

library_books

Host Genetic Variation Does Not Determine Spatio Temporal Patterns of European Bat 1 Lyssavirus

2017
Genome Biol Evol
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% […]

library_books

Spontaneous Loss of Virulence in Natural Populations of Listeria monocytogenes

2017
Infect Immun
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 […]

library_books

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

2017
PMCID: 5642193
PMID: 29056891
DOI: 10.1080/16546628.2017.1379861

[…] 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 […]


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

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