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

Author:

Seah Brandon K B1ORCID,Swart Estienne C1

Affiliation:

1. Max Planck Institute for Developmental Biology, Tübingen 72076, Germany

Abstract

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. Availability and implementation BleTIES is implemented in Python 3. Source code is available at https://github.com/Swart-lab/bleties (MIT license) and also distributed via Bioconda. Supplementary information Supplementary data are available at Bioinformatics online.

Funder

NSF

Max Planck Society

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

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