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To Trim or Not to Trim: Effects of Read Trimming on the De Novo Genome Assembly of a Widespread East Asian Passerine, the Rufous-Capped Babbler (Cyanoderma ruficeps Blyth)

1
Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
2
Division of Zoology, Endemic Species Research Institute, Nantou 552, Taiwan
*
Author to whom correspondence should be addressed.
Genes 2019, 10(10), 737; https://doi.org/10.3390/genes10100737
Received: 7 August 2019 / Revised: 17 September 2019 / Accepted: 20 September 2019 / Published: 23 September 2019
(This article belongs to the Section Animal Genetics and Genomics)
Trimming low quality bases from sequencing reads is considered as routine procedure for genome assembly; however, we know little about its pros and cons. Here, we used empirical data to examine how read trimming affects assembled genome quality and computational time for a widespread East Asian passerine, the rufous-capped babbler (Cyanoderma ruficeps Blyth). We found that scaffolds assembled from raw reads were always longer than those from trimmed ones, whereas computational times for the former were sometimes much longer than the latter. Nevertheless, assembly completeness showed little difference among the trimming strategies. One should determine the optimal trimming strategy based on what the assembled genome will be used for. For example, to identify single nucleotide polymorphisms (SNPs) associated with phenotypic evolution, applying PLATANUS to gently trim reads would yield a reference genome with a slightly shorter scaffold length (N50 = 15.64 vs. 16.89 Mb) than the raw reads, but would save 75% of computational time. We also found that chromosomes Z, W, and 4A of the rufous-capped babbler were poorly assembled, likely due to a recently fused, neo-sex chromosome. The rufous-capped babbler genome with long scaffolds and quality gene annotation can provide a good system to study avian ecological adaptation in East Asia. View Full-Text
Keywords: de novo genome assemble; reading trimming; rufous-capped babbler; computational time; genome quality de novo genome assemble; reading trimming; rufous-capped babbler; computational time; genome quality
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Yang, S.-F.; Lu, C.-W.; Yao, C.-T.; Hung, C.-M. To Trim or Not to Trim: Effects of Read Trimming on the De Novo Genome Assembly of a Widespread East Asian Passerine, the Rufous-Capped Babbler (Cyanoderma ruficeps Blyth). Genes 2019, 10, 737.

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