AdapterRemoval v2 is a major update of the previous version, offering significant improvements in throughput and functionality. It uses SIMD instructions (SSE1 and SSE2) and multi-threading to enhance performance. The tool can handle datasets with different adapters or adapter pairs, perform simultaneous demultiplexing and adapter trimming, and reconstruct adapter sequences from paired-end reads. It also supports native gzip and bzip2 compression. AdapterRemoval v2 shows superior throughput compared to other tools, both for single and multi-threaded operations. It is particularly suitable for processing large datasets and works well with longer reads from high-throughput sequencing platforms. The tool was evaluated against several other adapter trimming tools, showing high sensitivity and specificity for paired-end data. It also performs well in read merging. AdapterRemoval v2 can reconstruct adapter sequences from paired-end reads, which is useful for identifying experimental errors and analyzing poorly documented datasets. The tool is available under GPL v3 license and is implemented in C++. It is compatible with POSIX systems and requires zlib, libbzip2, and libpthreads for optional compression and multi-threading. The software is hosted on GitHub.AdapterRemoval v2 is a major update of the previous version, offering significant improvements in throughput and functionality. It uses SIMD instructions (SSE1 and SSE2) and multi-threading to enhance performance. The tool can handle datasets with different adapters or adapter pairs, perform simultaneous demultiplexing and adapter trimming, and reconstruct adapter sequences from paired-end reads. It also supports native gzip and bzip2 compression. AdapterRemoval v2 shows superior throughput compared to other tools, both for single and multi-threaded operations. It is particularly suitable for processing large datasets and works well with longer reads from high-throughput sequencing platforms. The tool was evaluated against several other adapter trimming tools, showing high sensitivity and specificity for paired-end data. It also performs well in read merging. AdapterRemoval v2 can reconstruct adapter sequences from paired-end reads, which is useful for identifying experimental errors and analyzing poorly documented datasets. The tool is available under GPL v3 license and is implemented in C++. It is compatible with POSIX systems and requires zlib, libbzip2, and libpthreads for optional compression and multi-threading. The software is hosted on GitHub.