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NxTrim specifications

Information


Unique identifier OMICS_05483
Name NxTrim
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 0.4.3
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline NxTrim <>

Additional information


https://github.com/sequencing/NxTrim/wiki

Publication for NxTrim

NxTrim in publications

 (16)
PMCID: 5934484
PMID: 29755426
DOI: 10.3389/fmicb.2018.00766

[…] with a paired-end approach and 301 cycles per read. reads were adapter-clipped and quality trimmed using trimmomatic (). mate-pair reads were additionally clipped, sorted and re-orientated using nxtrim (). potential phix and vector contamination were filtered out using fastq_screen, while low complexity reads (consisting entirely of only one base type or direct short oligonucleotide repeats) […]

PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w

[…] had a mean phred quality score >=30, 96% a mean phred quality score >=30 and 39% of sequences had an adapter sequence (either illumina or nextera, fig. ). adaptor trimming was performed with nxtrim for the mate pair library, followed by trimmomatic with the following options: minlen:40 illuminaclip:2:30:12:1:true leading:3 trailing:3 maxinfo:40:0.4 minlen:40 for both libraries. […]

PMCID: 5916287
PMID: 29721275
DOI: 10.1002/ece3.3918

[…] quality control was performed using the detailed guidelines provided by machado et al. () with some modifications. specifically, adapter trimming for mate‐pair sequences was performed using nxtrim v0.3.0‐alpha (o'connell et al., ), and all filtered reads were analyzed with fastuniq v1.1 (xu et al., ) to remove putative pcr duplications. the overall quality of all sequence reads […]

PMCID: 5814498
PMID: 29449404
DOI: 10.1128/genomeA.01594-17

[…] suite fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) identified some initial 5′ base bias, low-quality 3′ bases, and illumina adaptors, which were removed using trimmomatic (). nxtrim () was used for adaptor trimming of raw c. boidinii mate pair sequences. all sequences were error corrected and assembled using soapdenovo (). following genome masking, coding genes predicted […]

PMCID: 5784092
PMID: 29367590
DOI: 10.1038/s41598-018-19430-x

[…] to obtain approximately 136 million 150 bp pe reads (2 × 150 bp). we removed adaptor sequences using trimmomatic and the truseq3-pe adaptor file and removed reads shorter than 40 bp. we also used nxtrim to categorize the reads according to the orientation and adapter location and trim the circularizing adaptor., we used a biopsy of brain tissue and obtained high molecular weight dna using […]


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NxTrim institution(s)
Computational Biology Group and Technology Development, Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, Essex, UK

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