deML protocols

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deML specifications

Information


Unique identifier OMICS_06677
Name deML
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for deML

deML in pipelines

 (4)
2018
PMCID: 5784115
PMID: 29367746
DOI: 10.1038/s41598-018-20020-0

[…] illumina base-calling was performed using bustard. we trimmed illumina adapters and merged completely overlapping paired sequences using leehom and de-multiplexed the pooled sequencing data using deml., the sequencing data were aligned against the human reference genome hg19 using bwa’s aln algorithm and all sequence pairs that aligned to the nry region which are previously defined […]

2017
PMCID: 5692555
PMID: 29078328
DOI: 10.1073/pnas.1708341114

[…] of genes with a certain histone modification was significantly overrepresented in one of the resulting clusters., scrb-seq plate pools (i7) were demultiplexed from the illumina barcode reads using deml (). reads were mapped to the human genome (build hg38) using star 2.5 (). cell- and gene-wise unique molecular identifier (umi) tables were generated using the published drop-seq pipeline […]

2016
PMCID: 5110243
PMID: 27669147
DOI: 10.7554/eLife.18683.030

[…] on one lane of an illumina hiseq 2500 platform (rapid mode)., base-calling, adaptor trimming and demultiplexing of reads was performed using a custom pipeline based on freeibis (), leehom () and deml (). demultiplexed reads were mapped using tophat v2.0.14, and fpkm (fragments per kilobase of transcript per million mapped reads) values per gene were quantified using cufflinks v.2.2.1 (). […]

2016
PMCID: 5312299
PMID: 27463017
DOI: 10.18632/oncotarget.10827

[…] chimeric sequences were flagged as failing quality control and overlapping paired reads were merged using leehom with the “—ancientdna” option []. reads were assigned to their sample of origin using deml [] and jivebunny with default quality thresholds (https://github.com/udo-stenzel/biohazard). reads were then mapped to the human genome reference hg19 using bwa-0.4.9. library complexity […]


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deML in publications

 (5)
PMCID: 5784115
PMID: 29367746
DOI: 10.1038/s41598-018-20020-0

[…] illumina base-calling was performed using bustard. we trimmed illumina adapters and merged completely overlapping paired sequences using leehom and de-multiplexed the pooled sequencing data using deml., the sequencing data were aligned against the human reference genome hg19 using bwa’s aln algorithm and all sequence pairs that aligned to the nry region which are previously defined […]

PMCID: 5692555
PMID: 29078328
DOI: 10.1073/pnas.1708341114

[…] of genes with a certain histone modification was significantly overrepresented in one of the resulting clusters., scrb-seq plate pools (i7) were demultiplexed from the illumina barcode reads using deml (). reads were mapped to the human genome (build hg38) using star 2.5 (). cell- and gene-wise unique molecular identifier (umi) tables were generated using the published drop-seq pipeline […]

PMCID: 5312299
PMID: 27463017
DOI: 10.18632/oncotarget.10827

[…] chimeric sequences were flagged as failing quality control and overlapping paired reads were merged using leehom with the “—ancientdna” option []. reads were assigned to their sample of origin using deml [] and jivebunny with default quality thresholds (https://github.com/udo-stenzel/biohazard). reads were then mapped to the human genome reference hg19 using bwa-0.4.9. library complexity […]

PMCID: 5110243
PMID: 27669147
DOI: 10.7554/eLife.18683.030

[…] on one lane of an illumina hiseq 2500 platform (rapid mode)., base-calling, adaptor trimming and demultiplexing of reads was performed using a custom pipeline based on freeibis (), leehom () and deml (). demultiplexed reads were mapped using tophat v2.0.14, and fpkm (fragments per kilobase of transcript per million mapped reads) values per gene were quantified using cufflinks v.2.2.1 (). […]

PMCID: 4866544
PMID: 26454764
DOI: 10.1093/molbev/msv215

[…] sequencing (illumina miseq, paired end 2 × (150 bp + 7 bp)) and base calling (bustard, illumina), overlapping paired-end reads were merged using leehom (), tags associated with tfbs alleles using deml (), and the number of occurrences of each tag counted (supplementary table s3, supplementary material online)., all analyses were implemented in r (version 3.0.3) () using tinn-r (). replicates […]


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deML institution(s)
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, Germany

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