Abstract:
:Long sequencing reads offer unprecedented opportunities in analysis and reconstruction of complex genomic regions. However, the gain in sequence length is often traded for quality. Therefore, recently several approaches have been proposed (e.g. higher sequencing coverage, hybrid assembly or sequence correction) to enhance the quality of long sequencing reads. A simple and cost-effective approach includes use of the high quality 2nd generation sequencing data to improve the quality of long reads. We designed a dedicated testing procedure and selected universal programs for long read correction, which provide as the output sequences that can be used in further genomic and transcriptomic studies. Our results show that HALC is the best choice for correction of long PacBio reads, when both, read size and quality, are the main focus of the analysis. However, the tested tools show some unexpected behaviors, including read trimming and fragmentation.
journal_name
Genomicsjournal_title
Genomicsauthors
Mahmoud M,Zywicki M,Twardowski T,Karlowski WMdoi
10.1016/j.ygeno.2017.12.011subject
Has Abstractpub_date
2019-01-01 00:00:00pages
43-49issue
1eissn
0888-7543issn
1089-8646pii
S0888-7543(17)30166-0journal_volume
111pub_type
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