FLEXBAR—Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms

By Matthias Dodt, Johannes T. Roehr, R. Ahmed, Christoph Dieterich. Biology, 2012

689 citations recorded by the source corpus.

Quantitative and systems biology approaches benefit from the unprecedented depth of next-generation sequencing. A typical experiment yields millions of short reads, which oftentimes carry particular sequence tags. These tags may be: (a) specific to the sequencing platform and library construction method (e.g., adapter sequences); (b) have been introduced by experimental design (e.g., sample barcodes); or (c) constitute some biological signal (e.g., splice leader sequences in nematodes). Our software FLEXBAR enables accurate recognition, sorting and trimming of sequence tags with maximal flexibility, based on exact overlap sequence alignment. The software supports data formats from all current sequencing platforms, including color-space reads. FLEXBAR maintains read pairings and processes separate barcode reads on demand. Our software facilitates the fine-grained adjustment of sequence tag detection parameters and search regions. FLEXBAR is a multi-threaded software and combines speed with precision. Even complex read processing scenarios might be executed with a single command line call. We demonstrate the utility of the software in terms of read mapping applications, library demultiplexing and splice leader detection. FLEXBAR and additional information is available for academic use from the website: http://sourceforge.net/projects/flexbar/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d2f798b3716a2a5021bfdfb263564d56ccc3bdd8

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens (2016, neutral): “21 [46] (params: –adapter CTTTGTGTTTGA –adapter-trim-end LEFT –nono-length-dist –threads 4”
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads (2014, methodology): “Other adapter trimmers showed advantages on a specific metric; e.g. AdapterRemoval , Flexbar , and EA-Tools were the most sensitive, while TagCleaner , Btrim , and Scythe were the most conservative.”
Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots (2018, methodology): “Quality reads were demultiplexed based on the 137 barcode-primer sequences using flexbar [59].”
Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. (2014, methodology): “Tools like FLEXBAR (16) can be used to trim adaptor and barcode sequences before they are used as input for breseq .”
A Unified Model for the Function of YTHDF Proteins in Regulating m6A-Modified mRNA (2020, methodology): “A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript shorter than 18 nucleotides were then removed by using Flexbar with the default --min-readlength option (Dodt et al., 2012).”