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bbduk from bbmap v38.68  (Illumina Inc)


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    Structured Review

    Illumina Inc bbduk from bbmap v38.68
    Bbduk From Bbmap V38.68, 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/bbmap+bbduk/bbduk+from+bbmap+v38+68/pm37592350-35-25-0
    Average 90 stars, based on 1 article reviews
    bbduk from bbmap v38.68 - 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: Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation.
    Article Snippet: 10 Illumina reads were prepared by first trimming with BBMap v38.86 (bbduk.sh; 11 https://github.com/BioInfoTools/BBMap) using the settings ‘ktrim=r k=23 mink=11 hdist=1 tpe 12 tbo minlen=50 qtrim=rl trimq=30 maq=33 threads=40’.

    Article Title: Transcriptome of Taenia solium during in vitro cyst activation and initial growth into the tapeworm stage
    Article Snippet: Removal of Illumina adapter sequences and trimming of the reads with a phred + 33 quality score below 20 was done using BBDuk (BBMap version 38.90) .

    Article Title: Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation
    Article Snippet: Illumina reads were prepared by first trimming with BBMap v38.86 (bbduk.sh; https://github.com/BioInfoTools/BBMap ) using the settings “ktrim = r k = 23 mink = 11 hdist = 1 tpe tbo minlen = 50 qtrim = rl trimq = 30 maq = 33 threads = 40'.

    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: 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.

    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: Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation.
    Article Snippet: 10 Illumina reads were prepared by first trimming with BBMap v38.86 (bbduk.sh; 11 https://github.com/BioInfoTools/BBMap) using the settings ‘ktrim=r k=23 mink=11 hdist=1 tpe 12 tbo minlen=50 qtrim=rl trimq=30 maq=33 threads=40’.

    Article Title: Transcriptome of Taenia solium during in vitro cyst activation and initial growth into the tapeworm stage
    Article Snippet: Removal of Illumina adapter sequences and trimming of the reads with a phred + 33 quality score below 20 was done using BBDuk (BBMap version 38.90) .

    Article Title: Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation
    Article Snippet: Illumina reads were prepared by first trimming with BBMap v38.86 (bbduk.sh; https://github.com/BioInfoTools/BBMap ) using the settings “ktrim = r k = 23 mink = 11 hdist = 1 tpe tbo minlen = 50 qtrim = rl trimq = 30 maq = 33 threads = 40'.

    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: 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.



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