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BleTIES: Annotation of natural genome editing in ciliates using long read sequencing

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Seah,  BKB
Research Group Ciliate Genomics and Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Swart,  EC
Research Group Ciliate Genomics and Molecular Biology, Max Planck Institute for Developmental Biology, Max Planck Society;

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Citation

Seah, B., & Swart, E. (2021). BleTIES: Annotation of natural genome editing in ciliates using long read sequencing. Bioinformatics, 37(21): btab613, pp. 3929-3931. doi:10.1093/bioinformatics/btab613.


Cite as: https://hdl.handle.net/21.11116/0000-000A-3B30-E
Abstract
Summary: Ciliates are single-celled eukaryotes that eliminate specific, interspersed DNA sequences (internally eliminated sequences, IESs) from their genomes during development. These are challenging to annotate and assemble because IES-containing sequences are typically much less abundant in the cell than those without, and IES sequences themselves often contain repetitive and low-complexity sequences. Long read sequencing technologies from Pacific Biosciences and Oxford Nanopore have the potential to reconstruct longer IESs than has been possible with short reads, but require a different assembly strategy. Here we present BleTIES, a software toolkit for detecting, assembling, and analyzing IESs using mapped long reads.