AdapterRemoval v2 is a major update of the previous version, offering significant improvements in throughput and functionality. It utilizes SIMD instructions (SSE1 and SSE2) and multi-threading to enhance performance, allowing it to process large datasets more efficiently. The tool can handle datasets with varying adapter sequences or adapter pairs, and it supports simultaneous demultiplexing and adapter trimming. It also enables the reconstruction of adapter sequences from paired-end reads, which is particularly useful for poorly documented datasets. AdapterRemoval v2 also natively supports gzip and bzip2 compression, making it suitable for handling large files. Compared to existing tools, AdapterRemoval v2 demonstrates superior throughput, especially in multi-threaded operations. It maintains high sensitivity in adapter trimming, though specificity can be adjusted with command-line options. For paired-end reads, AdapterRemoval v2 achieves high sensitivity and specificity, making it highly effective for ancient DNA sequencing. In terms of read merging, it performs comparably to other tools, showing good sensitivity and specificity. The tool was benchmarked against several other adapter trimming and read merging programs, including AlienTrimmer, CutAdapt, leehom, PEAR, PEAT, fastq-mcf, FLEXBAR, Scythe, Skewer, and Trimmomatic. AdapterRemoval v2 outperformed many of these in throughput, particularly for merging overlapping reads. It also showed strong performance in reconstructing adapter sequences, although it lacks the ability to identify multiple, overrepresented sequences in single-end reads, which Minion can do. AdapterRemoval v2 is available under the GPL v3 license and is implemented in C++. It is compatible with POSIX systems, including Linux and macOS, and requires optional libraries for compression and multi-threading. The tool is well-suited for processing large datasets generated by high-throughput sequencing platforms, and its performance scales well with increasing read lengths. Overall, AdapterRemoval v2 is a powerful and efficient tool for adapter trimming, read merging, and data preprocessing in high-throughput sequencing workflows.AdapterRemoval v2 is a major update of the previous version, offering significant improvements in throughput and functionality. It utilizes SIMD instructions (SSE1 and SSE2) and multi-threading to enhance performance, allowing it to process large datasets more efficiently. The tool can handle datasets with varying adapter sequences or adapter pairs, and it supports simultaneous demultiplexing and adapter trimming. It also enables the reconstruction of adapter sequences from paired-end reads, which is particularly useful for poorly documented datasets. AdapterRemoval v2 also natively supports gzip and bzip2 compression, making it suitable for handling large files. Compared to existing tools, AdapterRemoval v2 demonstrates superior throughput, especially in multi-threaded operations. It maintains high sensitivity in adapter trimming, though specificity can be adjusted with command-line options. For paired-end reads, AdapterRemoval v2 achieves high sensitivity and specificity, making it highly effective for ancient DNA sequencing. In terms of read merging, it performs comparably to other tools, showing good sensitivity and specificity. The tool was benchmarked against several other adapter trimming and read merging programs, including AlienTrimmer, CutAdapt, leehom, PEAR, PEAT, fastq-mcf, FLEXBAR, Scythe, Skewer, and Trimmomatic. AdapterRemoval v2 outperformed many of these in throughput, particularly for merging overlapping reads. It also showed strong performance in reconstructing adapter sequences, although it lacks the ability to identify multiple, overrepresented sequences in single-end reads, which Minion can do. AdapterRemoval v2 is available under the GPL v3 license and is implemented in C++. It is compatible with POSIX systems, including Linux and macOS, and requires optional libraries for compression and multi-threading. The tool is well-suited for processing large datasets generated by high-throughput sequencing platforms, and its performance scales well with increasing read lengths. Overall, AdapterRemoval v2 is a powerful and efficient tool for adapter trimming, read merging, and data preprocessing in high-throughput sequencing workflows.