Flexbar protocols

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Flexbar specifications

Information


Unique identifier OMICS_01087
Name Flexbar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA, FASTQ
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 3.4.0
Stability Stable
Maintained Yes
Wikipedia https://github.com/seqan/flexbar/wiki

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  • person_outline Johannes Roehr <>

Publications for Flexbar

Flexbar in pipelines

 (32)
2018
PMCID: 5844307
PMID: 29378821
DOI: 10.1534/g3.117.300508

[…] san diego, ca)., data quality, including base quality per position across reads, gc content, and distribution of sequence length, was initially assessed with fastqc (). reads were processed with flexbar () in two passes: the first to trim adapters, remove low quality reads, and remove reads <35 bp in length, and the second to remove polya tails. subsequently, reads that mapped to fox […]

2018
PMCID: 5940794
PMID: 29739937
DOI: 10.1038/s41467-018-04219-3

[…] a custom pipeline was developed to de-multiplex and remove pcr and sequencing artefacts from the dblα sequence tags. reads were demultiplexed into individual fastq files for each isolate using flexbar v2.5 and paired based on valid combinations of molecular identifier (mid) tags in the forward and reverse reads. a minimum read length of 100nt and a maximum uncalled bases threshold of 15 […]

2017
PMCID: 5312088
PMID: 28196965
DOI: 10.1128/mBio.02348-16

[…] according to the workflow indicated by the provider. libraries were constructed followed by high-throughput sequencing to obtain paired-end reads with 151 bp in the forward and reverse directions., flexbar () was used to trim the adapter from the reads. prinseq () was employed (i) to trim the reads from the 3′ end until reaching the first nucleotide with a quality threshold of 20, (ii) […]

2017
PMCID: 5327466
PMID: 28240248
DOI: 10.1038/srep43495

[…] fc-401-4002) as single-end 100 nt-long reads. sequencing data were processed using the illumina pipeline software version 1.84. reads were right-trimmed for the illumina adapter sequence using flexbar (https://sourceforge.net/projects/flexbar/) and aligned with bowtie2. counting reads over annotated features was done with featurecounts. annotation was taken from tuberculist release r27. […]

2017
PMCID: 5394689
PMID: 28417974
DOI: 10.1038/srep45303

[…] as the reference sequence. we updated annotations of srnas in this genome sequence using the rfam 11.0 database. prior to mapping, we trimmed adapter sequences from illumina reads using flexbar 2.31. mapping was carried out in single-end mode using bowtie2 2.2.5 with the −k 1 option to achieve one unique mapping location per read. the raw number of reads mapping to each gene […]


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Flexbar in publications

 (81)
PMCID: 5940794
PMID: 29739937
DOI: 10.1038/s41467-018-04219-3

[…] a custom pipeline was developed to de-multiplex and remove pcr and sequencing artefacts from the dblα sequence tags. reads were demultiplexed into individual fastq files for each isolate using flexbar v2.5 and paired based on valid combinations of molecular identifier (mid) tags in the forward and reverse reads. a minimum read length of 100nt and a maximum uncalled bases threshold of 15 […]

PMCID: 5904416
PMID: 29666288
DOI: 10.1128/mBio.00575-18

[…] at the university of texas genomic sequencing and analysis facility (ut gsaf) on an illumina hiseq2000 system., hiseq reads were downloaded and concatenated, and adapters were removed using flexbar (v2.34) (), as described previously (). reads were trimmed to a minimum length of 18 bp or 30 bp, depending on the analysis. an absolute minimum length of 18 bp was selected for the pooled […]

PMCID: 5861125
PMID: 29559621
DOI: 10.1038/s41467-018-03575-4

[…] deficiency mutants. importantly, these controls are also effective when there is no prior knowledge of the expected binding behavior., uvclap libraries were demultiplexed and adapters removed using flexbar (version 2.32). barcodes and umis were extracted using custom scripts. to reliably remove readthroughs into barcode regions containing random and semi-random nucleotides, five nucleotides […]

PMCID: 5845876
PMID: 29563897
DOI: 10.3389/fmicb.2018.00294

[…] rdp extension to pandaseq () assembler () was used to merge the raw reads using a minimum overlap of 150 bp and a minimum phred score of 25. primer sequences were removed from the fastq files using flexbar version 2.5 (). sequences were converted to fasta format and concatenated into one file. sequence clustering was done using vsearch version 1.0.10 () at 97% identity and using usearch_global […]

PMCID: 5820273
PMID: 29463813
DOI: 10.1038/s41598-018-21478-8

[…] quantification kit, universal (kapa biosystems) prior to sequencing on an illumina highseq. 2500 with single-end 75 base read lengths. for the analysis of rna-seq, fastq files were trimmed using flexbar to remove 3′ bases with quality score lower than 30 before alignment as described previously. the trimmed reads were mapped to human genome version grch38 downloaded from gencode using hisat2 […]


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Flexbar institution(s)
Institute of Bioinformatics, FU Berlin, Berlin, Germany; Klaus Tschira Institute for Integrative Computational Cardiology / Department of Internal Medicine III, Heidelberg, Germany

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