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PRINSEQ++ is a C++ implementation of the very popular software prinseq-lite for quality control and preprocessing of sequencing datasets. PRINSEQ++ can run multi-threaded processes, which makes it more than 10 times faster than the original version. It can read from, and write to, compressed files, drastically reducing the use of hard-drive. PRINSEQ++ can filter, trim and reformat sequences by a variety of options to improve downstream analysis. PRINSEQ++ is freely available on GitHub (https://github.com/Adrian-Cantu/PRINSEQ-plus-plus) and runs on all Unix-like systems.
This is a preprint submission to PeerJ Preprints.
Raw data for timing experiment
Each row is a timing measurement for some input size/ number of threads combination
Each rows indicates the average time, standard deviation, standard error, and .95 confidence interval for the timing measurements for each input size/number of threads combination. This data is derived from sup_table1
Runtime comparison, Run-time of prinseq-lite and PRINSEQ++ was measured on several FASTQ pair files of different sizes with equivalent options. PRINSEQ++ was run with different number of threads, prinseq-lite single-threaded. Mean speedup of PRINSEQ++ ove