Nesoni protocols

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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 in pipelines

PMCID: 5767232
PMID: 29375506
DOI: 10.3389/fmicb.2017.02637

[…] (2-bp × 250-bp reads). raw reads were merged with seqprep using default settings, including the removal of sequencing adapters. reads that failed to merge were quality trimmed and filtered using nesoni v0.112. both merged and processed single reads were assembled using spades version 2.5.0 (), followed by manual curation of the assembly (). the reconstructed genome sequences of strains nd1 […]

PMCID: 5784116
PMID: 29367612
DOI: 10.1038/s41598-018-20015-x

[…] the illumina hiseq instrument (agrf, melbourne, australia), with hiseq. 2500 v4 chemistry. raw sequence reads from the 94 samples were assessed in fastqc v0.11.4 and hard trimmed to 100 bp using nesoni v0.132., the 94 nsw genomes were de novo assembled using spades v3.6.2. sequence read and assembly metrics are summarised in supplementary table . sequence read data for all nsw isolates […]

PMCID: 5826242
PMID: 29515540
DOI: 10.3389/fmicb.2018.00251

[…] genomic dna from each sample, using the nextera dna sample preparation kit., table shows the general information about the 26 samples used in this study., briefly, all samples were pre-processed by nesoni ( to remove low quality sequences and to trim adaptors, and afterwards assembled together using megahit (default parameters) (li […]

PMCID: 5578852
PMID: 28860254
DOI: 10.1128/genomeA.00902-17

[…] length of 4,057 bp (∼77-fold depth of coverage). illumina hiseq sequencing was used to generate 25,226,358 101-bp paired-end reads (∼354-fold depth of coverage). illumina adaptors were removed using nesoni:clip ( filtered illumina and pacbio reads were used to generate a hybrid de novo assembly using spades version 3.10.0 (), […]

PMCID: 5587575
PMID: 28878209
DOI: 10.1038/s41467-017-00342-9

[…] 500 bp). pooled library (12 pm) was loaded to a 600 cycles v3 reagent cartridge (illumina) and the sequencing was performed on hiseq (illumina)., raw sequence data was quality trimmed using the nesoni clip tool ( to remove the non-uniform coverage caused by the genome amplification step the samples were normalized to a coverage […]

Nesoni in publications

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 […]

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 […]

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 […]

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 () […]

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 […]

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