Repeat masking in MAKER2 (difference with BRAKER2)
1.9.1 Repeat masking in MAKER2 (difference with BRAKER2) For repeat masking, MAKER2 used the same repeat libraries (generated by RepeatModeler) as BRAKER2 (for details, see section 1.4.2 about repeat masking). It is important to note that even though MAKER2 and BRAKER2 used the same repeat libraries, genomes are masked differently by MAKER2 when comparing to our approach of using RepeatMasker/RepeatModeler for BRAKER2. MAKER2 runs RepeatMasker internally. Subsequently, MAKER2 does hard-masking of all interspersed (complex) repeats while low-complexity (simple) repeats remain soft-masked. Borders of complex repeats are extended by 50 nt. For the BRAKER2 run, the sequence was soft-masked with RepeatMasker. Within BRAKER2, AUGUSTUS uses information on soft-masked regions at the gene prediction step and reduces the probability of coding exon prediction in repeat regions. GeneMark-ES and -EP+ do hard-masking of soft-masked repeats longer than 1000 nt for genomes shorter than 300 Mb and they do hard-masking of soft-masked repeats longer than 100 nt for genomes longer than 300 Mb.
https://academic.oup.com/nargab/article/3/1/lqaa108/6066535#supplementary-data
- 发表于 2022-11-10 10:46
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- 分类：基因组学
