Flexbar protocols

Flexbar specifications

Information


Unique identifier OMICS_01087
Name Flexbar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License BSD 3-clause “New” or “Revised” License, GNU General Public License version 2.0
Computer skills Advanced
Version 3.0.3
Stability Stable
Source code URL https://codeload.github.com/seqan/flexbar/tar.gz/v3.0.3
Maintained Yes
Wikipedia https://github.com/seqan/flexbar/wiki

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Publications for Flexbar

Flexbar IN pipelines

 (19)
2018
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 previously49. the trimmed reads were mapped to human genome version grch38 downloaded from gencode50 using […]

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 bowtie219. counting reads over annotated features was done with featurecounts20. annotation was taken from tuberculist release […]

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

[…] 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 bowtie219. counting reads over annotated features was done with featurecounts20. annotation was taken from tuberculist release r27. to avoid the influence of transcripts […]

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

[…] as the reference sequence38. we updated annotations of srnas in this genome sequence using the rfam 11.0 database39. prior to mapping, we trimmed adapter sequences from illumina reads using flexbar 2.3140. 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 read41. the raw number of reads mapping to each gene […]

2017
PMCID: 5570135
PMID: 28472469
DOI: 10.1093/nar/gkx355

[…] the profiles were smoothed by applying the cubic spline interpolation. more than 2-fold enrichment was considered as significant., adapter sequences were removed from the reads using flexbar tool (37). sequencing data for ‘mock’, piwi rip or piwi rip after actinomycin d treatment were mapped to the dm3/r5 genome assembly by ‘bowtie2’ (33). for the exonic read counting, […]

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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