RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation.

ABSTRACT:

Summary

Repetitive elements comprise large proportion of many genomes. They have impact on both genome evolution and regulation. Their classification and the study of evolutionary history is a major emerging field. Various software exist to-date to classify and map repeats across genomes. The major unresolved drawback, however, is the fragmented nature of many identified repeat loci. This ultimately makes the classification of novel repeats and their evolutionary analyses difficult. To improve on this, we developed a pipeline (RepeatCraft) that integrates results from several repeat element classification tools based on both sequence similarity and structural features. The pipeline de-fragments closely spaced repeat loci in the genomes, reconstructing longer copies, thus allowing f

SUBMITTER: Wong WY 

PROVIDER: S-EPMC6419915 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature