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Nesoni specifications


Unique identifier OMICS_07362
Name Nesoni
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


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Nesoni citations


Taxon Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient

Front Microbiol
PMCID: 5943556
PMID: 29774016
DOI: 10.3389/fmicb.2018.00869

[…] to first discard methodological biases including sequencing artifacts, we pre-processed data for quality filtering, chimeric sequences, homopolymers, and short reads (cutoff: 50 bp) using the nesoni clip tool ( version 0.133. overall, the quality of forward reads (r1) was better than reverse reads (r2). this difference is related […]


Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

Front Microbiol
PMCID: 5904459
PMID: 29696004
DOI: 10.3389/fmicb.2018.00680

[…] and illumina hiseq 2500 (rmr5) sequencing platforms, respectively., metagenome sequence reads were clipped to remove adaptor sequences and low quality bases (phred score 15, min. length 50 bp) using nesoni. quality trimmed reads were uploaded to the mg-rast platform () for phylogenetic and functional whole-community classification. phylogenetic classification was performed by blat-based […]


A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

PMCID: 5885306
PMID: 29632618
DOI: 10.1186/s13100-018-0118-3

[…] database []. the sra-toolkit (fastq-dump utility) [] was used to download paired-end next generation sequencing reads and convert them from .sra files to interleaved fastq files. we then used nesoni (; last accessed march 2018) to prune all known adapters, cleave bases with a phred quality score of 10 or lower, and exclude reads […]


Concurrent Host Pathogen Transcriptional Responses in a Clostridium perfringens Murine Myonecrosis Infection

PMCID: 5874911
PMID: 29588405
DOI: 10.1128/mBio.00473-18

[…] nc_003366 and nc_003042) using shrimp alignment software (). the number of reads aligning to each genome location, including the open reading frames and intergenic regions, was determined using nesoni ( the coverage plot for each sample was then generated by nesoni and was visualized in the artemis genome browser () […]


5′ Rapid Amplification of cDNA Ends and Illumina MiSeq Reveals B Cell Receptor Features in Healthy Adults, Adults With Chronic HIV 1 Infection, Cord Blood, and Humanized Mice

Front Immunol
PMCID: 5879793
PMID: 29632541
DOI: 10.3389/fimmu.2018.00628

[…] a bitscore <75 that indicates a match to less than 50 bp of bcr sequence. we also used the igblast results to orient the paired-end reads. poor quality bases with qscore ≤3 were clipped using nesoni clip that also removed reads with <25 bp remaining in either end. we then merged paired-end reads having ≥10 bp overlap with at least 90% identity, or having 9–19 bp overlap with at least […]


Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements

PLoS Genet
PMCID: 5882170
PMID: 29565971
DOI: 10.1371/journal.pgen.1007292

[…] an ion chef instrument (thermo fisher). sequencing was performed using the ion proton system (thermo fisher). read sets from technical repetitions were combined. adapter sequences were removed using nesoni clip ( to reduce any potential rrna/total-rna abundance biases introduced during rrna depletion, reads mapping to rrna genes […]

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