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bbduk.sh script  (Illumina Inc)


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    Structured Review

    Illumina Inc bbduk.sh script
    Bbduk.Sh Script, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/bbduk%2Esh+script/bbduk+sh/pm39835612-39-9-2
    Average 90 stars, based on 1 article reviews
    bbduk.sh script - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Next-Generation Sequencing:

    Article Title: Microbiome Signatures and Inflammatory Biomarkers in Culture-Negative Neonatal Sepsis
    Article Snippet: The demultiplexed read pairs underwent an initial quality filtering using bbduk.sh (BBMap, version 38.82) [23], removing Illumina adapters, PhiX reads, and reads with a Phred quality score < 15 and length < 100 bp after trimming.

    Article Title: Mechanism of Forced-Copy-Choice RNA Recombination by Enteroviral RNA-Dependent RNA Polymerases
    Article Snippet: Results from NGS used the following pipeline for analysis: data was evaluated with FastQC, trimmed with bbduk.sh (BBmap suite) to remove adapter sequences (both Illumina universal and small RNA adapter), sequences were clustered using clumpify.sh (BBMap suite), each sequence was treated differently which did not allow any substitutions, and the top 500 sequences identified (sequence, count, and length).

    Article Title: Responses of fungal diversity and community composition after 42 years of prescribed fire frequencies in semi-arid savanna rangelands
    Article Snippet: As a result, all the primers and adapters were removed from the amplicon sequences using the bbduk. sh script using the following parameter options: llumine ASAP/illumina-adapters-all.fasta, ktrim = r, k = 19, mink = 11, hdist = 1, minlen = 80, ottm = t, ordered = t, stats = samplename-fastqstats.txt, and statscolumns = 5.

    Article Title: The impact of spray-induced gene silencing on cereal phyllosphere microbiota.
    Article Snippet: Raw Illumina paired-end reads were demultiplexed with Sabre2 [59] and adapters were trimmed with the bbduk. sh script [60].

    Article Title: The impact of spray-induced gene silencing on cereal phyllosphere microbiota
    Article Snippet: Raw Illumina paired-end reads were demultiplexed with Sabre2 [ ] and adapters were trimmed with the bbduk.sh script [ ].

    Article Title: Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice.
    Article Snippet: Raw reads were preprocessed with bbduk.sh to trim reads and remove adapter sequences, specifically Illumina Nextera adapters, using the following parameters: ktrim = r, k = 23, mink = 11, hdist = 1, minlength = 50, tpe, and tbo.

    Article Title: Probiotic treatment induces sex-dependent neuroprotection and gut microbiome shifts after traumatic brain injury.
    Article Snippet: Demultiplexed read pairs underwent an initial quality filtering using bbduk.sh (BBMap version 38.82), removing Illumina adapters, PhiX reads and reads with a Phred quality score below 15 and length below 100 bp after trimming.

    Article Title: Circumpolar Population Structure, Diversity and Recent Evolutionary History of the Bearded Seal in Relation to Past and Present Icescapes.
    Article Snippet: The raw Illumina sequence reads were trimmed using the bbduk.sh script from bbmap v.39.01 (Bushnell 2014) with the filters ktrim = r, k = 23, mink = 8, hdist = 1, tbo, qtrim = rl, trimq = 15, maq = 20, and minlen = 40.

    Sequencing:

    Article Title: Microbiome Signatures and Inflammatory Biomarkers in Culture-Negative Neonatal Sepsis
    Article Snippet: The demultiplexed read pairs underwent an initial quality filtering using bbduk.sh (BBMap, version 38.82) [23], removing Illumina adapters, PhiX reads, and reads with a Phred quality score < 15 and length < 100 bp after trimming.

    Article Title: Mechanism of Forced-Copy-Choice RNA Recombination by Enteroviral RNA-Dependent RNA Polymerases
    Article Snippet: Results from NGS used the following pipeline for analysis: data was evaluated with FastQC, trimmed with bbduk.sh (BBmap suite) to remove adapter sequences (both Illumina universal and small RNA adapter), sequences were clustered using clumpify.sh (BBMap suite), each sequence was treated differently which did not allow any substitutions, and the top 500 sequences identified (sequence, count, and length).

    Article Title: Responses of fungal diversity and community composition after 42 years of prescribed fire frequencies in semi-arid savanna rangelands
    Article Snippet: As a result, all the primers and adapters were removed from the amplicon sequences using the bbduk. sh script using the following parameter options: llumine ASAP/illumina-adapters-all.fasta, ktrim = r, k = 19, mink = 11, hdist = 1, minlen = 80, ottm = t, ordered = t, stats = samplename-fastqstats.txt, and statscolumns = 5.

    Article Title: The impact of spray-induced gene silencing on cereal phyllosphere microbiota.
    Article Snippet: Raw Illumina paired-end reads were demultiplexed with Sabre2 [59] and adapters were trimmed with the bbduk. sh script [60].

    Article Title: The impact of spray-induced gene silencing on cereal phyllosphere microbiota
    Article Snippet: Raw Illumina paired-end reads were demultiplexed with Sabre2 [ ] and adapters were trimmed with the bbduk.sh script [ ].

    Article Title: Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice.
    Article Snippet: Raw reads were preprocessed with bbduk.sh to trim reads and remove adapter sequences, specifically Illumina Nextera adapters, using the following parameters: ktrim = r, k = 23, mink = 11, hdist = 1, minlength = 50, tpe, and tbo.

    Article Title: Probiotic treatment induces sex-dependent neuroprotection and gut microbiome shifts after traumatic brain injury.
    Article Snippet: Demultiplexed read pairs underwent an initial quality filtering using bbduk.sh (BBMap version 38.82), removing Illumina adapters, PhiX reads and reads with a Phred quality score below 15 and length below 100 bp after trimming.

    Article Title: Circumpolar Population Structure, Diversity and Recent Evolutionary History of the Bearded Seal in Relation to Past and Present Icescapes.
    Article Snippet: The raw Illumina sequence reads were trimmed using the bbduk.sh script from bbmap v.39.01 (Bushnell 2014) with the filters ktrim = r, k = 23, mink = 8, hdist = 1, tbo, qtrim = rl, trimq = 15, maq = 20, and minlen = 40.



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