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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Maintainer


  • person_outline Johannes Roehr <>

Flexbar articles

Flexbar citations

 (3)
2017
PMCID: 5582413

[…] libraries were then clustered at a concentration of 8 pmol, and sequencing was performed 2x100bl on a hiseq2000 (illumina, san diego, usa) sequencer., all reads were trimmed and quality clipped with flexbar (dodt et al, 2012). all remaining reads (> 18 bp in length) were mapped against the murine 45s rrna precursor sequence (bk000964.3) to remove rrna contaminant reads. we used the mouse […]

2017
PMCID: 5777333

[…] onto the nextseq 500 flow cell at a final concentration of 1.8 pm., demultiplexed and quality filtered raw reads (fastq) generated from the nextseq 500 were trimmed to remove adaptor sequences using flexbar 2.4 and aligned to the s. cerevisiae genome (s288c, saccer3) from the saccharomyces genome database60 using tophat version 2.0.961. ht seq-count version 0.6.1 was used to generate gene counts […]

2017
PMCID: 5394689

[…] 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 […]

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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