flexbar

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The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences.

exonerate

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Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

cutadapt

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cutadapt removes adapter sequences fromnhigh-throughput sequencing data. This is usually necessary when the readnlength of the sequencing machine is longer than the molecule that isnsequenced, for example when sequencing microRNAs.