AdapterRemoval: easy cleaning of next-generation sequencing reads

By Stinus Lindgreen. BMC Research Notes, 2012

602 citations recorded by the source corpus.

With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts of data generated. One recurring problem is adapter contamination in the reads, i.e. the partial or complete sequencing of adapter sequences. These adapter sequences have to be removed as they can hinder correct mapping of the reads and influence SNP calling and other downstream analyses. We present a tool called AdapterRemoval which is able to pre-process both single and paired-end data. The program locates and removes adapter residues from the reads, it is able to combine paired reads if they overlap, and it can optionally trim low-quality nucleotides. Furthermore, it can look for adapter sequence in both the 5’ and 3’ ends of the reads. This is a flexible tool that can be tuned to accommodate different experimental settings and sequencing platforms producing FASTQ files. AdapterRemoval is shown to be good at trimming adapters from both single-end and paired-end data. AdapterRemoval is a comprehensive tool for analyzing next-generation sequencing data. It exhibits good performance both in terms of sensitivity and specificity. AdapterRemoval has already been used in various large projects and it is possible to extend it further to accommodate application-specific biases in the data.

Subfields: Cancer Research, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/977b070e2ba6f8756239156c3c1476f2e2dbd03b

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Citations in the corpus

Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX (2014, methodology): “The correct sequences must be used to prevent contaminating the final sequences with the adapter sequences 50 .”
Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli (2014, methodology): “For both phylogenetic approaches, sequence data were initially quality trimmed using the program AdapterRemoval (30), keeping only reads of a minimum length of 20 nucleotides (nt) and a quality score of at least 30 and without N=s.”
Trimmomatic: a flexible trimmer for Illumina sequence data (2014, methodology): “In this scenario, AdapterRemoval performed particularly well, reflecting its relative strength in removing technical sequences.”
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads (2014, unknown): “Other adapter trimmers showed advantages on a specific metric; e.g. AdapterRemoval , Flexbar , and EA-Tools were the most sensitive, while TagCleaner , Btrim , and Scythe were the most conservative.”