AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3′ end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.
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Schubert M, Lindgreen S, Orlando L.
AdapterRemoval v2: rapid adapter trimming, identification, and read merging.
BMC Res Notes. 2016 Feb 12;9:88. doi: 10.1186/s13104-016-1900-2. PMID: 26868221; PMCID: PMC4751634.