AdapterRemoval protocols

AdapterRemoval specifications


Unique identifier OMICS_01081
Name AdapterRemoval
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes



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Publication for AdapterRemoval

AdapterRemoval IN pipelines

PMCID: 5743481
PMID: 29299249
DOI: 10.1002/ece3.3553

[…] paired‐end sequenced on illumina miseq platform at the danish national high‐throughput dna sequencing centre., the dataset consisted of 27,073,487 paired‐end reads. raw reads were processed using adapterremoval (lindgreen, 2012), trimming low‐quality bases, and discarding reads shorter than 30 bp. only collapsed reads with an overlap of 11 bp were used for downstream analysis. reads […]

PMCID: 5798962
PMID: 29219730
DOI: 10.1080/15476286.2017.1403003

[…] 10 billion. the average sampling depths of the serum and technical replicate samples were 17.9 and 19.5 million raw reads, respectively. the reads were initially trimmed for adapters using adapterremoval v2.1.7 [77]. we then mapped the collapsed reads (generated by fastx v0.14) to the human genome (hg38) using bowtie2 v2.2.9 (10 alignments per read were allowed). we compiled […]

PMCID: 4776208
PMID: 26907326
DOI: 10.3390/v8020053

[…] python script to partition the reads based on exact matches in the fastq header lines to the multiplexed indices provided. preprocessing of reads was performed for all datasets in parallel using adapterremoval [43] with the following parameters {--trimns, --trimqualities, --minquality 2, --minlength 30, --collapse, --outputcollapsed, --outputcollapsedtruncated, --singleton}. read ends […]

PMCID: 4776208
PMID: 26907326
DOI: 10.3390/v8020053

[…] read in a pair was kept as a singleton. overlapping paired reads from short inserts were collapsed into a single read if the overlap was longer than 11 bp, according to the default behaviour of adapterremoval., preprocessed reads were filtered if they showed homology to the human reference genome, which included decoys and alternative sequences from version gca_000001405.15 (grch38) […]

PMCID: 5039028
PMID: 27668515
DOI: 10.7554/eLife.17092.043

[…] was built (gansauge and meyer, 2013) and sequenced on an illumina hiseq 2500. of the 282,924 reads sequenced, 68,204 remained after quality filtering and filtering for reads larger than 30 bp using adapterremoval (lindgreen, 2012). remaining reads were mapped to an ostrich reference nuclear and mitochondrial genomes (zhang et al., 2015) using bwa-aln (version: 0.7.5a-r405) with default settings […]

AdapterRemoval institution(s)
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

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