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Structured Review

Lexogen GmbH bbduk bbmap version 37.87
Bbduk Bbmap Version 37.87, supplied by Lexogen GmbH, 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+of+bbmap/bbduk/pm39433949-342-5-15
Average 90 stars, based on 1 article reviews
bbduk bbmap version 37.87 - by Bioz Stars, 2026-11
90/100 stars

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Related Articles

other:

Article Title: Renal fibroblasts are involved in fibrogenic changes in kidney fibrosis associated with dysfunctional telomeres.
Article Snippet: Read adaptors and poly(A) tails were removed with the command ‘bbduk.sh’ according to the Lexogen recommendations.

Article Title: Multi-omic spatial profiling reveals the unique SARS-CoV-2 lung microenvironment and collagen VI as a predictive biomarker in severe COVID-19.
Article Snippet: Background: Whilst COVID-19 is primarily a respiratory infection, few studies have characterized the immune response to COVID-19 in lung tissue.. We sought to understand the pathogenic role of microenvironmental interactions and the extracellular matrix in post-mortem COVID-19 lung using an integrative multi-omic approach.. Methods: Post-mortem formalin fixed paraffin embedded lung tissue from fatal COVID-19 and non-respiratory death control lung underwent multi-omic evaluation by Quantseq Bulk RNA sequencing, Nanostring GeoMX spatial transcriptomics, RNAscope, multiplex immunofluorescence and immunohistochemistry, to evaluate virus distribution, immune composition and the extracellular matrix.

Article Title: Mitochondrial mechanotransduction through MIEF1 coordinates the nuclear response to forces.
Article Snippet: The reads were trimmed using BBDuk (BBMap version 37.87) with the parameters indicated in the Lexogen data analysis protocol.

Article Title: Genet identity and season drive gene expression in outplanted Acropora palmata at different reef sites
Article Snippet: Demultiplexing was done by the sequencing facility, and raw reads had adapters and low-quality reads trimmed using BBDuk.sh with recommended parameters from Lexogen ( https://www.lexogen.com/quantseq-data-analysis ).

Article Title: Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders
Article Snippet: Reads were then trimmed with bbduk and aligned to hg38-GENCODEv42 using STAR with the Lexogen recommended parameters for QuantSeq.

Sequencing:

Article Title: Paternal starvation affects metabolic gene expression during zebrafish offspring development and lifelong fitness.
Article Snippet: .. Following Lexogen guidelines, sequencing adapters, polyA read through and low- quality tails were removed by using the bbduk tool of the bbmap package (parameters: k = 13, ktrim = r, useshortkmers = t, mink = 5, qtrim = r, trimq = 10, minlength = 20) (Bushnell, 2014). ..

Article Title: Integrated immunogenomic analyses of high-grade serous ovarian cancer reveal vulnerability to combination immunotherapy
Article Snippet: .. For raw sequencing data of the cell lines, single-end reads were processed by trimming adapter and low-quality sequences using BBDuk with the parameters specified by Lexogen. ..

Article Title: Integrated immunogenomic analyses of high-grade serous ovarian cancer reveal vulnerability to combination immunotherapy.
Article Snippet: .. For sequencing data of the cell lines, single-end reads were processed by trimming adapter and low-quality sequences using BBDuk with the parameters specified by Lexogen. ..



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