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chevron_left Normalization Known transcript quantification Differential expression Bioinformatics workflows Data analysis Adapter trimming Gene expression visualization Read alignment visualization chevron_right
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READemption specifications


Unique identifier OMICS_05473
Name READemption
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Roche
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Konrad Forstner
  • person_outline Cynthia Sharma

Publication for READemption

READemption citations


Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches

Front Microbiol
PMCID: 5641341
PMID: 29067007
DOI: 10.3389/fmicb.2017.01941

[…] Reads in FASTQ format were trimmed with a cut-off Phred score of 20 by the program fastq_quality_trimmer from FASTX toolkit. The following steps were performed with the tool READemption (). The poly(A)-tail sequences (introduced in the library preparation) were removed and a size filtering step was performed that eliminated reads shorter than 12 nt. The remaining reads we […]


Analysis of host microRNA function uncovers a role for miR 29b 2 5p in Shigella capture by filopodia

PLoS Pathog
PMCID: 5398735
PMID: 28394930
DOI: 10.1371/journal.ppat.1006327
call_split See protocol

[…] Library preparation and deep-sequencing was performed by Vertis Biotechnology AG, as described previously []. RNA-seq analysis was performed using the READemption pipeline version 0.3.0 [], with Segemehl version 0.1.7 []. Reads were mapped against the human (build GRCh37) and Shigella flexneri (NCBI Reference Sequence NC_008258) genomes. Analysis of […]


Resolving host–pathogen interactions by dual RNA seq

PLoS Pathog
PMCID: 5313147
PMID: 28207848
DOI: 10.1371/journal.ppat.1006033

[…] f this originating from rRNA and tRNA loci. However, since genome composition varies tremendously across the bacterial phylogeny, potential cross-mapping should be a routine quality control step. The READemption RNA-seq analysis pipeline [], which relies on the segemehl read mapper [], contains alignment subcommands implementing such cross-mapping analysis. In principle, any read mapper capable of […]


Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases

PMCID: 5312081
PMID: 28196958
DOI: 10.1128/mBio.02041-16

[…] pping and quality trimming with cutadapt (, the reads were mapped to the AR9 genome sequence (KU878088) and the B. subtilis 168 genome sequence (NC_000964.3) with READemption version 0.3.0 () and segemehl version 0.1.7 (). For data visualization, graphs representing the number of mapped reads per nucleotide were calculated and normalized to the total number of […]


In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non coding RNA Pathways

Mol Cell
PMCID: 5222698
PMID: 28061332
DOI: 10.1016/j.molcel.2016.11.002
call_split See protocol

[…] was synthesized using oligo(dT)-adaptor and M-MLV reverse transcriptase. The linear amplified cDNAs were multi-plexed and sequenced using Illumina HiSeq. Reads were mapped to Salmonella genome using READemption; 5′ end coverage was visualized in IGB. The RNase E sites, which are depleted 5′ ends in the rneTS samples relative to WT at 44°C, were identified using DESeq2. […]


Cell differentiation defines acute and chronic infection cell types in Staphylococcus aureus

PMCID: 5595439
PMID: 28893374
DOI: 10.7554/eLife.28023.031

[…] y(A) removal, size filtering (minimum read length of 12 nucleotides after clipping), statistics generation, coverage calculation and normalization, which were performed with the RNA-analysis pipeline READemption version 0.3.3. READemption uses segemehl version 0.1.7 for the read alignment to the reference and DESeq 1.18.0 () (RRID:SCR_000154) for the differential gene expression analysis. The refe […]

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READemption institution(s)
Institute for Molecular Infection Biology and Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg, Germany
READemption funding source(s)
Supported by the Bavarian Research Network for Molecular Biosystems (BioSysNet), the BMBF eBio grant RNAsys and DFG project VO 875/4-2, the ZINF Young Investigator program at the Research Center for Infectious Diseases (ZINF, Wurzburg, Germany), DFG project Sh580/1-1, and the Young Academy program of the Bavarian Academy of Sciences.

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