<i>MaskerAid</i> : a performance enhancement to RepeatMasker

TLDR

Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence, but current repeat identification software is sensitive yet slow, creating a costly bottleneck in large‑scale analyses. MaskerAid enhances RepeatMasker by optimizing its algorithm to accelerate masking. This improvement yields a speed increase of more than 30‑fold at the most sensitive setting. MaskerAid is available on request from the authors (http://sapiens.wustl.edu/MaskerAid) and can be contacted at [e-mail].

Abstract

Abstract Summary: Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence. Current repeat identification software is sensitive but slow, creating a costly bottleneck in large-scale analyses. We have developed MaskerAid , a software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting. Availability: On request from the authors (see http://sapiens.wustl.edu/MaskerAid). Contact: [e-mail] These authors contributed equally to this work. * To whom correspondence should be addressed. ** Current address: Incyte Genomics, 4633 World Parkway Cir., St. Louis, MO 63134 USA, [e-mail]