Segemehl statistics

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Segemehl specifications


Unique identifier OMICS_00683
Name Segemehl
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.3.0
Stability Stable
Maintained Yes


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  • person_outline Steve Hoffmann <>

Publications for Segemehl

Segemehl in pipelines

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

[…] (, 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 reads. the resulting wiggle […]

PMCID: 5398735
PMID: 28394930
DOI: 10.1371/journal.ppat.1006327

[…] 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 differential gene expression was performed […]

PMCID: 5554785
PMID: 28787591
DOI: 10.1016/j.devcel.2017.07.002

[…] obtained from the qpcr analysis. sequencing was performed in hiseq2500 with using single end 50 bp reads., sequencing reads were aligned to the ws220/ce10 assembly of the c. elegans genome using segemehl version 2.0 () with 80% sequence similarity. samtools was used to convert aligned reads to bam format. after mapping, the genome coverage was calculated for all individual sample replicates. […]

PMCID: 5561264
PMID: 28819222
DOI: 10.1038/s41598-017-08806-0

[…] quality data were removed from the sequencing raw data using trimmomatic (version 0.32) (parameters: illuminaclip: adaptor.fa:2:30:10 leading:3 trailing:3 slidingwindow:4:15 minlen:50). the software segemehl (v 0.1.7) and ciri (v 2.0.5) were used for potential back-splice sites extraction, ., total rna was isolated by trizol reagent (life technologies, carlsbad, ca) followed by dna residue […]

PMCID: 5587724
PMID: 28878244
DOI: 10.1038/s41467-017-00539-y

[…] 3′ adapter trimming (5′-tggaattctcgggtgccaagg-3′) and quality control using the fastx-toolkit ( reads were then mapped to the yeast genome (saccer3) using segemehl (version 0.1.7–411), allowing a minimum mapping accuracy of 90%. chip peaks were found with macs (version 1.4.2) using the mapped reads from input and gcn4-chip samples as follows:macs14 -t […]

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Segemehl in publications

PMCID: 5875010
PMID: 29592812
DOI: 10.1186/s13059-018-1415-3

[…] and si-pcpb1-treated cells were downloaded from sra (accession srp022151) and converted to fastq format. reverse complemented and duplicate-collapsed reads were then mapped to the human genome with segemehl version 0.1.7 []. we did not use star for these data sets because these libraries, generated by drs (direct rna sequencing) had a high fraction of short reads that star did not map. […]

PMCID: 5865726
PMID: 29570714
DOI: 10.1371/journal.pone.0194438

[…] []. read quality was controlled using fastqc, adapter and low-quality reads were removed using bbduk from the bbmap software suite ( reads were mapped using segemehl version 2.0 []. multimapper and pcr duplicates were removed from further analysis. read end position were accumulated using bedtools multicov []. tpm-values (transcripts per million values) […]

PMCID: 5852086
PMID: 29540679
DOI: 10.1038/s41467-018-03369-8

[…] image analyses and base callings used the standard illumina pipeline. the tophat2 package was used to align reads to the hg19 reference genome, followed by deseq2 for rna expression analysis., the segemehl aligner (v0.2.0-418) was used in split-read mode, without realignment, to detect rna-sequenced split-transcript reads, defined as reads in which the left part aligned to the downstream […]

PMCID: 5856525
PMID: 29487214
DOI: 10.1073/pnas.1714718115

[…] was carried out by vertis biotechnologie, germany. all protocols were identical to those used previously (, ). sequence reads were mapped against the s. typhimurium d23580 reference genome using segemehl, with accuracy set to 100% (, ). rna-seq and drna-seq data can be downloaded as raw reads (.fastq file format); the gene expression omnibus database accession no. is gse108104., methods used […]

PMCID: 5831913
PMID: 29657296
DOI: 10.3390/ncrna3040025

[…] from the plantgdb database) to find those mapping to intergenic positions. in this step, the sugarcane transcripts classified as protein-coding and as lncrnas were mapped using the software segemehl []. those lncrnas mapping to regions between two genes were considered good lincrna candidates. an svm model was also used to identify sugarcane lincrnas, and the output from this model […]

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Segemehl institution(s)
Junior Research Group Transcriptome Bioinformatics, University Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics and Bioinformatics Group, University Leipzig, Leipzig, Germany; LIFE Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany; Department of Theoretical Chemistry, University Vienna, Vienna, Austria; RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology – IZI, Leipzig, Germany; Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany; Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark; Santa Fe Institute, Santa Fe, NM, USA; Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany; Department of Epidemiology and Biostatistics, Imperial College London, London, UK
Segemehl funding source(s)
Supported by LIFE (Leipzig Research Center for Civilization Diseases), Leipzig University and the Deutsche Forschungsgemeinschaft under the auspicies of SPP 1590 “Probabilistic Structures in Evolution”, proj. no. STA 850/14-1.

Segemehl review

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Rodman M X

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Quite resource demanding (time and RAM), but great tool. Especially if it comes to splice site prediction, circular RNA.